Many children with autism have had lab test results that show high levels of aluminum, mercury, copper and other metals, and a study by the California Department of Health Services found that "Air pollution [particularly metals and chlorinated solvents] boosts autism risk by 50 percent in newborns". Based on these 2 findings, metal toxicity certainly seems to be involved in the development of autism.
So if there is a genetic vulnerability, (which does seem to exist based on fraternal vs identical twin studies), it seems to me that genetic conditions that cause impaired metal efflux would be a logical starting point. A genetic metal efflux problem could explain why some children's bodies are not able to filter out the metals in the vaccines, and would therefore suffer health problems following vaccinations, while other children don't appear to have any problems.
The reports of many parents who witnessed their children regress soon after being vaccinated, in my opinion absolutely sounds like some type of injury. A healthy brain just does not lose previously aquired skills without being damaged by something. In fact, "The etiology of many neurodegenerative diseases has been only partly attributed to acquired traits, suggesting environmental factors may also contribute. Metal dyshomeostasis causes or has been implicated in many neurodegenerative diseases."
The NNii reports that children's aluminum levels exceed the minimal risk level after being vaccinated, but they're not concerned about that because "50-70% of injected aluminum [from vaccines] is excreted within 24 hours". That's a pretty big difference. So some children in their study still had 50% of the aluminum in their bodies the next day while others had only 30%. I would be very interested to know what percentage of this aluminum the children with autism were able to excrete. I would hypothesize that children with autism probably excreted even less aluminum than the group that was studied. (To see how much aluminum various vaccines contain, click here.)
- A high copper to zinc ratio is believed to cause many health issues such as mental problems, diabetes, decreased digestive enzyme activity, food sensitivities and allergies, and autoimmune diseases, IBS, and chronic candida. 
- "Mild zinc deficiency contributes to impaired physical and neuropsychological development and increased susceptibility to life-threatening infections in young children." 
That finding could help explain why zinc supplements and GF/CF diets are so beneficial for many children with autism. (Too little copper and too much zinc is not safe either, so ALWAYS consult with a doctor you trust before giving your children supplements or changing their diets.)
1. Zinc and Copper compete for absorption:
- "High intake of zinc induces the intestinal synthesis of a copper-binding protein called metallothionein. Metallothionein traps copper within intestinal cells and prevents its systemic absorption" 
- "The excess Cu results in impaired Zn absorption" 
2. Gluten and Casein affect Zinc and Copper levels:
- "Grains (especially wheat and gluten grains) inhibit zinc absorption. Dairy and calcium slows elimination of copper" 
- "Calcium in combination with phytic acid reduces zinc absorption", and "Phytic acid is present in legumes, grains, and rice" 
"Excessive copper can be neurotoxic, and ASD (Autism Spectrum Disorder) children typically have already-elevated levels of copper for the same reasons that their bodies cannot detoxify the other heavy metals (mercury, lead, etc.)" 
The following study found that only 4 out of 503 autism-spectrum patients did not exhibit a serious metal-metabolism disorder:
Abnormal Metal-metabolism throughout the autism spectrum
Autistic Disorder (318)
PDD with Autistic Features (162)
Asperger's Disorder (23)
>The incidence and severity of metal imbalances were very similar across these autism phenotypes.
The test subjects were selected from a pool of 705 patients previously diagnosed with an autistic-spectrum disorder. Using DSM-IV subjects with questionable diagnoses, and patents with co-morbidity for seizures, depression, schizophrenia, serious head injury, Tourette's Syndrome, and birth anoxia were excluded (deprived of oxygen).
Abnormal Metal-metabolism Observed in Test Subjects
- extremely disordered levels of Cu and Zn, indicating absence of blood homeostasis for these metals in 428 subjects (85%),
- moderately disordered Cu/Zn levels despite ongoing zinc therapy in 41 subjects (8%)
- Severe pyrrole disorder in an additional 30 subjects (6%) indicating severe zinc depletion
>These data strongly suggest a universal metallothionein protein dysfunction in autism-spectrum patients www.bbbautism.com/dan_william_walsh.htm
"Primary Functions of Metallothionein:
-Development of brain neurons
-Homeostatic control of Zn and Cu
-Detoxification of heavy metals
-Maturation of the GI tract
-Delivery of Zn to cells
Notes: When mercury binds to MT it leaves the body easily. It is a marvelous antioxidant in the body – when MT is down, the radicals are loose. " 
"MTs (metallothioneins) increase the resistance of cells to exposure to high Cu (copper) levels." 
"Metallothionein functions include neuronal development, detoxification of heavy metals, and immune response." 
>Children with autism have delayed neuronal development, high levels of heavy metals, and weaker immune systems.
Wilson's Disease causes excessive copper levels. "The protein ATP7B is important in the vesicular pathway of hepatic copper transport into bile. The WD gene mutation leads to absence or diminished function of ATP7B, resulting in a decrease in biliary copper excretion" 
On one blog a parent said his child's uremic copper level was so high the doctor wanted to do further testing to rule out Wilson's Disease. However, this condition is usually tested for by looking at the patient's ceruloplasmin concentration, and not by genetic testing because no quick genetic test has been developed yet. Unfortunately, the ceruloplasmin test is not a reliable method for ruling out the possibility of a child being a heterozygous carrier of Wilson's Disease since, "low serum ceruloplasmin concentrations may occur in up to 20% of asymptomatic WD heterozygotes".  So 80% of the time, a child who does have one copy of this gene would still have normal ceruloplasmin levels.
When I first heard about Wilson's disease 3 years ago, I never thought that autism and Wilson's Disease could be related because Wilson's Disease (the homozygous form) is very rare and causes liver problems and Kayser-Fleischer rings in the patient's eyes. However, after I learned that many children with autism have high copper to zinc ratios I decided to research Wilson's Disease more closely, and what I learned shocked me:
1. Wilson's Disease (the homozygous form where the person has 2 copies of this gene) is rare, but "Wilson's Disease is the most common of a group of hereditary diseases that cause copper overload in the liver" 
1 out of 100 people are heterozygous carriers for Wilson's Disease.  That's almost the same percentage as the current autism rate.
2. Even though most adults who are heterozygous carriers of WD are asymptomatic, CHILDREN with only one copy of the gene were found to have reduced serum copper levels with high uremic copper levels and neurological symptoms. (Just like many children with autism.) Here's the study:
"This paper reports on a study of the heterozygous children of patients with Wilson's disease. A total of 16 children of 10 patients with the disease were followed up. Detailed biochemical, clinical and EEG tests were done. Nearly all the children were found to have reduced serum copper and caeruloplasmin levels and high rates of urine copper excretion following exposure to penicillamine. These findings were different from the results obtained in adult heterozygous carriers. Thirty per cent of the children had pathological neurological findings, and EEG abnormalities were found in 75%." 
3. Wilson's Disease IS a mitochondrial disorder that causes encephalopathy and depletes metallothionein.  And "patients with Wilson's disease have relevant glutathione depression, with low levels of reduced glutathione and cysteine and high concentrations of oxidized glutathione [just like many children with autism]. This is prevented by zinc administration, which inhibits lipid peroxidation and increases glutathione availability." 
4. This study found that Wilson's disease may involve more than just copper:
"Interaction of trace metal metabolism was studied in a patient with Wilson's dease. Atomic absorption analysis showed markedly increased urinary excretion of copper and aluminum and an increased ALUMINUM content was found in the biopsied liver by neutron activation analysis. These findings suggest a complicated pathogenetic mechanism involving other metals besides copper in the Wilson's disease." 
5. "The Wilson's disease gene (ATP7B) has been mapped to chromosome 13 (13q14.3) and is expressed primarily in the liver, kidney, and placenta. The gene codes for a P-type (cation transport enzyme) ATPase that transports copper into bile and incorporates it into ceruloplasmin. Mutations can be detected in 90% of patients. Most (60%) are homozygous for ATP7B mutations (two abnormal copies), and 30% have only one abnormal copy. 10% have no detectable mutation." 
Compare that to this finding about the placentas of children who developed autism:
"They found that the placentas from ASD children were three times more likely to have the [trophoblast] inclusions... We knew that trophoblast inclusions were increased in cases of chromosome abnormalities and genetic diseases, but we had no idea whether they would be significantly increased in cases of ASD," said Kliman. "These results are consistent with studies by others who have shown that ASD has a clear genetic basis." 
Could the trophoblast inclusions be indicative of the ATP7B gene mutation that causes Wilson's Disease?
6. Wilson's disease can cause parkinsonism and schizophrenia-like symptoms, and a family history of these disorders is believed to increase a child's risk of developing autism. Here's a report about a man who was misdiagnosed with paranoid schizophrenia (and he also suffered from parkinsonism) until it was discovered 12 years later that he really had Wilson's Disease: HERE "The clinical presentation and therapeutic response of this patient strongly suggest a link between the cerebral intoxication by copper and the psychiatric symptoms." 
7. This website even suggests treating autism by following the same steps used to treat Wilson's Disease:
"A Lesson From Wilson's Disease
-Wilson's disease is copper overload disease which disables MT
-Two-phase treatment is effective
Step 1: removal of excess Cu
Step 2: long-term maintenance using Zn therapy – in Autism need to remove all metals.
>Autism therapy requires removal of Cu and toxic metals" 
8. Another study found that "Haplotypes in AKR1A1, COMT, ATP7A and ATP7B (Where the WD gene is located) also showed association with autism." 
There have already been environmental studies linking heavy metals in pollution to autism. However, not every child in these polluted areas has autism. So wouldn't a disease that causes the body to store excessive amounts of metals be a logical genetic risk?
And even if it's not specifically the same mutation seen in heterozygous carriers for "Wilson's Disease", 300 mutations of the Wilson's Disease gene have been identified, and perhaps the ATP7B gene (or some other gene in the ATPase gene family) could give researchers a clue of what genes should be studied. Furthermore, "A normal variation in the PRNP gene can modify the course of [Wilson's Disease] disease by delaying the age of onset and affecting the type of symptoms that develop. This gene produces prion protein, which is active in the brain and other tissues and also appears to be involved in transporting copper." 
One potential problem with this theory is the incidence of autism is higher in boys than girls, but Wilson's Disease affects men and women equally. However, I don't think that should rule out heterzygous WD as a potential cause that's worth researching. It is highly possible that the genetic susceptibility could be gender neutral, and it is the triggers which are gender specific. Consider the following studies:
- A trigger that affects males: This CDC study that found that among males, increased prenatal exposure (and increased exposure from birth to 7 months) to thimerosal was associated with, "poorer performance with attention and executive functioning", but "there were no significant associations for females". Here
- A trigger that affects females: This CDC study found that "Low birth weight and preterm birth increase the risk of autism in infants by about twofold, but more so for girls than for boys. ... When the 565 boys and girls with autism were looked at separately, the boys had less than a twofold increased risk of autism if they were born at low birth weight, but the low-birth-weight girls had a threefold or higher risk". Here.
The 2 findings above could help explain the higher incidence of autism in boys than girls because the thimerosal in the flu shot is given to most pregnant women and babies over 6 months, but most babies are not born prematurely.
(And it's also possible that some other factor is causing the low zinc levels, which would also result in low metallothionein production, high copper levels, and a weakened immune system. So some research will need to be done to determine which comes first; the the excess copper storage or the low zinc levels.)
IMPORTANT: I'm NOT suggesting that children with autism have Wilson's disease (the homozygous form that causes liver problems). I'm just asking if these children could have one copy of the WD gene, which might make them more susceptible to environmental toxins (such as the metals in vaccines) than their peers. So if your child has autism, please don't worry about the problems typically seen in Wilson's Disease. This is still only a theory, and most heterozygous carriers of WD are asymptomatic. However, being a heterozygous carrier of some diseases can make you more susceptible to environmental triggers than the general population. So I'm wondering if children with one copy of the gene would have also been asymptomatic if not for all the toxins in vaccines... That would also mean that in the absence of further vaccinations, and with the addition of supplemental zinc therapy, there probably wouldn't be any further regression or worsening of health problems.
"People with only one abnormal gene are called carriers (heterozygotes) and may have mild, but medically insignificant, abnormalities of copper metabolism." 
However, with the heterozygous form of some diseases these "insignificant" abnormalities can be significantly exacerbated by an environmental trigger. For an example of what I mean, lets look at Factor V Leiden deficiency. If you have 2 copies of this gene your risk of venous thrombosis is 80%, but if you have one copy your risk is only 5-7%. HOWEVER, when you add an environmental trigger, in this example it's oral contraceptives, the risk of venous thrombosis jumps up to 30-35% for people with heterozygous Factor V Lieden deficiency. The normal population's risk when taking oral contraceptives is only 4%.
So clearly, this medicine is not safe for people with the heterozygous form of this disease. And interestingly enough, this is also an example of a genetic mutation that occurs in men and women equally, but has a gender-specific trigger (since men don't take OCPs).
My daughter has heterozygous Factor V, but the ONLY reason we know that is because one of her aunts had problems with blood clots, which eventually led to the Factor V diagnosis and a recommendation that all family members should be tested. If not for the advice to have genetic testing done, we may have found that my daughter has this condition the hard way; after she developed a blood clot due to OCPs.
The point I'm trying to make is that heterozygous Wilson's Disease doesn't seem to cause problems in general. However, studies have shown that children who are heterozygous carriers of Wilson's Disease do have problems with metal-homeostasis, and therefore it is quite reasonable to wonder if receiving mulitple doses of vaccines that contain toxic metals like aluminum and mercury would cause health problems in this genetically subsceptible group.
"It should be noted that individuals with genetic disorders affecting copper metabolism (e.g., Wilson's disease, Indian childhood cirrhosis, and idiopathic copper toxicosis) may be at risk for adverse effects of chronic copper toxicity at significantly lower intake levels [than the tolerable level of intake for the general population]." 
1. The FDA found that Aluminum was Causing Neurological Delays in Premature Babies and Dementia in Kidney Dialysis Patients. AND the FDA found that "Aluminum toxicity is difficult to identify in infants because few reliable techniques are available to evaluate bone metabolism in premature infants. . . Although aluminum toxicity is not commonly detected clinically, it can be serious in selected patient populations, such as NEONATES, and may be more common than is recognized." As a result of this finding, the FDA requires IV feeding solutions to contain no more than 25 mcg of aluminum per liter of solution. The Hep B vaccine given to newborns contains 250 mcg of aluminum...
Some people argue that the amount of aluminum in vaccines is safe because soy baby formula contains much more aluminum than the vaccines. HOWEVER, "Only a minute proportion of the aluminium we ingest from these various sources is absorbed by the body", but vaccines are injected into muscle tissue where 100% of the contents are absorbed and have to be filtered out by the kidneys. This explains why the FDA's limit for injectable solutions is 25 mcg, but extra-strength antacid tablets still contain 160,000 mcg (labeled on the package as 160 mg).
2. Aluminum Causes Dementia
"IT IS NOW GENERALLY ACCEPTED that aluminum is the toxic etiological factor in the dialysis encephalopathy syndrome. The mechanism by which aluminum acts as a neurotoxin is not clearly defined. It has been proposed that aluminum acts as a neurotoxin by inhibition of dihyropteridine reductase. This would reduce the brain content of tetrahydrobiopterin, tyrosin and neuro-transmitters. The neurotoxicity of aluminum alternatively may involve alterations in the major postsynaptic enzymes of cholinergic neurotransmission. Aluminum inhibits choline transport in erythrocytes and decreases choline acetyltransferase activity in nerve tissue. Aluminum has also been reported to inhibit cytosolic and mitochondrial hexokinase activities in rat brain and thus reduce carbohydrate utilization. The concentrations of aluminum used in these latter experiments were comparable to those found in the brains of patients who had died from dialysis encephalopathy."
3. Dialysis dementia was first proposed to be "due to aluminum intoxication because they found increased aluminum content in brain, muscle, and bone tissues of affected patients; the brain gray-matter aluminum content was higher in ALL of their patients with the [dialysis dementia] syndrome than in any of the controls or other uremics." 
Keeping that in mind, I wonder if this next finding is just a coincidence or does it suggest causalty?
"In the normal brain, larger amounts of gray matter are associated with higher IQs," Dr. Ashtari said. "But in the autistic brain, increased gray matter does not correspond to IQ, because this gray matter is not functioning properly."
4. Aluminum Affects Mitochondrial Functions
"Aluminum toxicity is associated with mitochondrial dysfunction and the production of react: Compared with the control treatment without Al, the accumulation of Al in tobacco cells caused instantaneously the repression of mitochondrial activities [monitored by the reduction of 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide and the uptake of Rhodamine 123] and, after a lag of about 12 h, triggered reactive oxygen species (ROS) production, respiration inhibition, ATP depletion, and the loss of growth capability almost simultaneously. The presence of an antioxidant, butylated hydroxyanisol, during Al treatment of SL cells prevented not only ROS production but also ATP depletion and the loss of growth capability, suggesting that the Al-triggered ROS production seems to be a cause of ATP depletion and the loss of growth capability. Furthermore, these three late events were similarly repressed in an Al-tolerant cell line (ALT301) isolated from SL cells, suggesting that the acquisition of antioxidant functions mimicking butylated hydroxyanisol can be a mechanism of Al tolerance. In the pea root, Al also triggered ROS production, respiration inhibition, and ATP depletion, which were all correlated with inhibition of root elongation. Taken together, we conclude that Al affects mitochondrial functions, which leads to ROS production, probably the key critical event in Al inhibition of cell growth." 
"Reactive oxygen species (ROS) are ions or very small molecules that include oxygen ions, free radicals, and peroxides, both inorganic and organic. They are highly reactive due to the presence of unpaired valence shell electrons. ROS form as a natural byproduct of the normal metabolism of oxygen and have important roles in cell signaling. However, during times of environmental stress [neurotoxins in vaccines??] ROS levels can increase dramatically, which can result in significant damage to cell structures. This cumulates into a situation known as oxidative stress. They are also generated by exogenous sources such as ionizing radiation." 
Many children with autism have high levels of oxidative stress and depleted ATP.
5. Aluminum Toxicity causes neurological delays and thin bones. Children with autism have both of these symptoms. The CDC says that large amounts of aluminum have been shown to cause neurological and skeletal delays in unborn and developing animals.  The CDC also cites a study that found a "statistically valid" association between children with autism and thin bones. This study said that even the boys who were NOT on a casein-free diet had thinner bones than the control group. This surprised the researchers because they expected the group with autism to have thicker bones since they on average weighed more than the control group.  Aluminum that is absorbed by the body is usually excreted in the urine or deposited in bone, "which acts as a 'sink' to remove aluminium". 
6. In 1983, children were only given 5 doses of aluminum-containing vaccines by 2 years. Now, children receive 18 doses by 18 months (13 doses by 6 months). Use of this much aluminum in babies is too new to say that there is a proven record of safety. For information on which vaccines contain aluminum and when they were added to the schedule, click here.
7. Aluminum Damages the Blood Brain Barrier
"Our present studies suggest that aluminum increases the permeability of BBB by changing its ultrastructure and the expression of occludin and F-actin. Zinc can protect the integrity of BBB in juvenile rats that are exposed to aluminum and inhibit the decrease of tight junction protein occludin and F-actin expression in BBB." 
Children with an impaired metal efflux ability would have more trouble than their peers eliminating the aluminum in vaccines, and most children with autism have low zinc levels, which would leave their BBB's unprotected against the damaging effects of the aluminum that accumulates in their systems. This combinination could conceivably make this subgroup of the population extremely vulnerable to the neurotoxic metals in vaccines.
Additionally, children with autism also have low concentrations of metallothionein, which is necessary for detoxifying heavy metals and for immune function. Weakened immune function would also make these children more vulnerable than their peers to live-virus vaccines.
Even though the MMR does not contain aluminum or mercury, it does contain LIVE measels virus and other toxic ingredients. So giving this vaccine to a child whose BBB is damaged (more permeable), AND who has a weakened immune system, sounds pretty dangerous to me.
Wilson's Disease patients have low blood copper levels and high urine copper levels, and they also have low zinc levels. This study found that "lower levels of maternal blood copper were significantly associated with higher cadmium concentrations in cord blood. Placental cadmium in women with lower levels of maternal blood zinc was significantly higher than in those with normal zinc levels. " 
So a child whose mother has a high copper to zinc ratio would be exposed to higher levels of cadmium prenatally. Increased cadmium is NOT a good thing, that's for sure. "Cadmium has no constructive purpose in the human body. It, and its compounds, are extremely toxic even in low concentrations, and will bioaccumulate in organisms and ecosystems." 
Because 1 out of 100 people are heterozygous carriers of Wilson's disease, AND because a high copper to zinc ratio in pregancy is dangerous, regular monitoring of prenatal uremic copper and zinc levels may be warranted. (Copper levels that are too low are dangerous too, so always consult with your doctor before making any health decision.)
This study hypothesized that mothers who are heterozygous carriers of Wilson's disease could have high Cu:Zn ratios while pregnant which could result in autism or schizophrenia of the child later in life: "Therefore, the developing fetus of a pregnant women who is low in Zn and high in Cu may experience major difficulties in the early development of the brain, which may later manifest themselves as schizophrenia, autism or epilepsy. Similarly, a person who gradually accumulates Cu, will tend to experience a gradual depletion of Zn, with a corresponding increase in oxidative damage," 
However, I suspect it's more likely that an elevated maternal Cu:Zn ratio could help to explain the cases of classic autism, and that regressive autism could occur in children who have an impaired metal efflux ability. Children who accumulate toxic metals from vaccines and pollution and who have depleted zinc levels would quite conceivably suffer from oxidative damage.
An elevated maternal Cu:Zn ratio could possibly explain the cases of classic autism (where the symptoms were present at birth) because the baby would have had high prenatal exposure to neurotoxic metals. This group of children may or may not inherit this gene from their mothers if the mother only has one copy of the gene that causes Wilson's Disease.
A genetic metal efflux disorder could cause children to accumulate more toxic metals than their peers. With regressive autism, could it be possible that the mother's Cu:Zn ratio was fine, but the child inherited one copy of the Wilson's Disease gene from the father, and therefore had no symptoms until being given several vaccines which exceeded the child's metallothionein reserves? David Kirby's lecture series reports that the gene inheritance pattern for the MtD link in autism seems to be strongly paternal. 
The fraternal versus identical twin studies show a strong genetic association, but the incidence of autism occuring in both identical twins is not 100%. That proves environmental factors are also important. While identical twins typically would have an almost identical environment, some possible variables are diet and health status at the time of vaccination.
Diets can affect zinc levels and even identical twins may prefer different foods or eat different amounts of foods. Also, all infants and children are at risk for zinc deficiency, and severe diarrhea can cause zinc deficiency in people of any age.  So infants and children with severe diarrhea would probably have VERY low levels of zinc, which results in low levels of metallothionein. Therefore, if one twin was moderately ill or not yet fully recovered from an illness at the time of vaccination, that twin might be more likely to suffer an adverse reaction than the healthy twin.
Since all infants and children share this risk of a zinc deficiency, even children with no genetic susceptibility could be also be at risk of suffering a severe vaccine reaction if their zinc levels are very low and they are given too many vaccines for their weakened immune systems to handle.
1. All newborns should be screened for this condition, and if found to be positive,then they should NOT be given today's current vaccines with high metal contents (except for the Hep B vaccine IF the baby's mother has Hep B). Also, PLEASE note that 1 out of 100 adults has one copy of this gene with NO symptoms. So this finding should not (and I pray that it will not) lead to an explosion of abortions, because finding that your child does have one copy of this gene doesn't mean that he or she has autism. What it would imply is that today's current vaccine schedule is probably too toxic and too excessive for your child, and he or she should NOT be vaccinated according to the current schedule.
2. Zinc supplementation really seems to help (both patients with WD and Autism). "Metallothionein concentrations increased by 1500% after zinc and 150% after penicillamine in Wilson's disease patients, with respect to controls who had negative endoscopy and Wilson's disease patients who were not treated. A significant correlation was found between metallothionein and duodenal zinc concentrations.
Zinc administration increases intestinal metallothionein in Wilson's disease patients. The blockade of copper absorption and its elimination in the stools on desquamation of the intestinal cells probably explains one of the mechanisms underlying the effect of zinc treatment. Despite normal endoscopy, Wilson's disease patients present increased mucosal iron concentrations similar to those in controls with duodenitis. Metallothionein may therefore prevent oxidative damage caused by metal toxicity." 
3. Also, Heterozygous Wilson's disease is believed to be a risk factor for Parkinson's disease, and this site (here) reports successful treatments for Parkinson's disease from using ethical adult stem cells. These stem cells are taken directly from the patient so there is no risk of rejection, and adult stem cells have already helped treat many conditions (unlike embryonic stem cells which have a high risk of tumor formation and genetic mutations. ) Here's one Parkinson's patient's personal story: Here. BUT I don't know if this could help patients with autism, so please don't try this without consulting a reputable doctor first.
UPDATE as of 4-12-09:
4. Some people have reported that Citicoline has been a helpful treatment for autism, which is very interesting as Citicoline has produced some very promising results for Alzheimer's Disease patients:
"The present data indicate that Citicoline (1,000 mg/day) is well tolerated and improves cognitive performance, cerebral blood perfusion and the brain bioelectrical activity pattern in AD patients. According to our results, it seems that citicoline might be a useful treatment in Alzheimer's disease, and that the efficacy of this compound is greater in patients with mild mental deterioration and/or bearing the epsilon 4 allele of the APOE." 
I find the association between Citicoline (a form of Choline) and autism VERY interesting because the following study found that aluminum "seriously worsened" learning ability AND led to "diminished cholinergic activity, which is a characteristic of Alzheimer's disease." [Here]
5. Other people have reported some very promising results from using IV glutathione pushes. The idea that this treatment would be helpful is quite logical since children with autism tend to have low levels of glutathione, frequent infections, and significantly elevated levels of toxins such as mercury and aluminum. Glutathione is required for both fighting viruses and excreting toxins.
6. For more information on treating autism, you may want to read Healing and Preventing Autism: A Complete Guide by by Jenny McCarthy and Dr. Jerry Kartzinel
IMPORTANT: Always consult a reputable doctor before making any medical decision. A good DAN! doctor should be able to advise which treatments would be best for a child with autism and the safest methods for applying these treatments.
Alter the vaccine schedule.
1. Regardless of genetic vulnerabilities I think giving the flu shot to pregnant women, babies, and young children is a bad idea based on this CDC study that found that among males, increased prenatal exposure to thimerosal was associated with, "poorer performance with attention and executive functioning" Here There was a large increase in the autism percentage rate when the flu shot was first recommended for pregnant women. 
2. Also, the FDA set a limit of 25 mcg for injectable solutions because aluminum was causing neurological delays in preemies, so WHY is the 250 mcg Hep B vaccine given to all newborns INCLUDING premature babies?? This study found that "Low birth weight and preterm birth increase the risk of autism in infants by about twofold, but more so for girls than for boys".  Estrogen is believed to increase absorption of certain metals, which might explain why girls in this category would have a higher risk. (Babies born to mothers that are Hep B positive do NEED this vaccine, but most newborns do not.)
Vaccines contain dangerous ingredients, and therefore should only be given when clearly needed - just like antibiotics. Antibiotics used to be prescribed flippantly, but now we know overuse of antibiotics causes resistant strains of bacteria. So now doctors are strongly urged to only prescribe antibiotics when "clearly needed". Likewise, I believe vaccines should only be administered when the benefits clearly outweigh the risk. Here's a few suggested changes:
1. This study from the Harvard Cancer Center (here), found that having a health history of mumps parotitis actually decreases a woman's chance of developing ovarian cancer. So preventing girls from contracting the mumps could actually be increasing their risk of developing ovarian cancer. Since actually contracting the disease gives you life-long immunity and because mumps is such a mild disease for children I think the mumps vaccine should not be given to children. However, since mumps is dangerous for older males the vaccine should be given to pre-adolescent boys who have never had the mumps.
2. I think the Rotateq vaccine should NOT be on the mandated AAP schedule. In America, the benefits do not outweigh the risks of this vaccine. The 1998 version of this vaccine (Rotashield) caused severe intestinal damage and death (here). Also, it's a live-virus vaccine and I'm concerned this vaccine will actually cause more cases of rotavirus. There have been cases where children recently vaccinated against chicken pox actually caused an outbreak of chicken pox at their day care centers.
3. I also think the chicken pox vaccine should not be on the schedule either. It's a very mild disease for children but more difficult for adults. Unlike the actual disease, the vaccine does not provide lifelong immunity, and the vaccine even increases the risk of developing shingles. So children are better off actually catching the disease.
4. Since all babies and children are at risk of zinc deficiency, AND because they have immature immune, neurological, and renal systems, we should only give the most crucial shots to children under 2 years of age. Back in 1983, children only received 10 shots (for 7 diseases) by their 2nd birthday. Now in 2008 children are given 34 shots (for 14 diseases) by 2 years: Here. Think back to 1983. Did you hear about children in the U.S. dying from epidemics? On the other hand, now a child is diagnosed with autism every 20 minutes (72 kids every day), and almost everyone knows someone who has a child with autism. Additionally, we may not have childhood diseases anymore, but now children are suffering from significantly higher rates of severe food allergies, asthma, juvenile diabetes, cancer, and brain diseases like bi-polar disorder and ADHD. I'd rather have a temporary illness (such as the flu, mumps, chicken pox, or rotavirus), than any of those chronic lifelong diseases.
Everything has a toxic limit so we should not give our children 10,000 - 100,000 vaccines at once as Paul Offit has claimed would be fine.  Half of our children's vaccines contain more than 100 mcg of aluminum. Mulitply 100 mcg times 5,000 vaccines and you get 500,000 mcg of aluminum. (and 100 mcg times 50,000 vaccines = 5,000,000 mcg of aluminum!!) That cannot be safe. Remember, the FDA set a limit of 25 mcg for injectable medical solutions. If vaccines continue to be added to the childhood immunization schedule, eventually the amount of toxic ingredients in vaccines will be dangerous for all children -- even without a genetic susceptibility.
Disclaimer: Some vaccines are worth getting so ALWAYS consult with a doctor before making any medical decision.
I think we should "Green our vaccines", administer them at a slower schedule, REMOVE unncessary vaccines from the schedule (but they could still be available for parents who want them), and personally, I think we should also "Humane our vaccines". The means by which human fetal tissue was obtained for vaccine purposes is horrific, and unnecessary. Here. Regardless of your personal opinion of abortion, I'm sure we'd all agree that if a child is born alive as the result of a prostoglandin abortion, they should not have to endure this heinous attrocity: "50% of the time, the baby would be born alive, but that didn't stop them. They would just simply open up the abdomen of the baby with no anesthesia, and take out the liver and kidneys, etc."  I don't know if Merck or the other vaccine manufacturers will ever change their current vaccines, but a company named AVM biotechnologies has pledged to make ethical vaccines. Perhaps they could find a way to make them safer too? http://www.cogforlife.org/avm.htm