Follow this line of research then, looking at mercury exposure as causing a dysfunctional immune response to pathogens, microbes -- ie viral/bacterial.

"Mercury (Hg) has been shown to have immunotoxic effects and to influence the severity of infection."

"...virus persistence tended to be influenced by MeHg in a direction compatible with the development of chronic disease."

"The evidence presented here clearly indicates that Hg acts as an immunotoxicant by dysregulating physiologically appropriate responses to stimuli, suggesting that Hg exposure may lead to similar dysregulation of the immune response to pathogens in exposed persons."

"This is the first study to report immunologic changes, indicative of autoimmune dysfunction in persons exposed to mercury, which may also reflect interactions with infectious disease and other factors"

"Vaccines, in several reports were found to be temporally followed by a new onset of autoimmune diseases. The same mechanisms that act in infectious invasion of the host, apply equally to the host response to vaccination."

Following the trail, we can see how issues with mitochondria can also be involved with both mercury/thimerosal and the immune system:

"Chronic MeHg exposure results in ultrastructural changes and accumulation of MeHg within mitochondria"

"The results of this study suggest that ethylmercury is a mitochondrial toxin in human astrocytes. We believe that this finding is important, particularly since the number of diseases in which mitochondrial dysfunction has been implicated are rapidly increasing."

Mitochondria in innate immune responses.

"The innate immune system has a key role in the mammalian immune response. Recent research has demonstrated that mitochondria participate in a broad range of innate immune pathways, functioning as signalling platforms and contributing to effector responses. In addition to regulating antiviral signalling, mounting evidence suggests that mitochondria facilitate antibacterial immunity by generating reactive oxygen species and contribute to innate immune activation following cellular damage and stress. Therefore, in addition to their well-appreciated roles in cellular metabolism and programmed cell death, mitochondria appear to function as centrally positioned hubs in the innate immune system."

"Increasing evidence of autoimmune phenomena in individuals with autism could represent the presence of altered or inappropriate immune responses in this disorder, and this immune system dysfunction may represent novel targets for treatment."

Which brings us to the Amerian Academy of Pediatrics:

AAP 2001: "Mercury in all of its forms is toxic to the fetus and children, and efforts should be made to reduce exposure to the extent possible to pregnant women and children as well as the general population."

AAP 2003: Addressing Parents’ Concerns: Do Vaccines Cause Allergic or Autoimmune Diseases?

Paul A. Offit, MD, Charles J. Hackett, PhD:

"Autoimmune diseases might occur after immunization because proteins on microbial pathogens are similar to human proteins (“molecular mimicry”) and could induce immune responses that damage human cells.....Theoretically, if infections can trigger autoimmune diseases, modified forms of infections (ie, immunizations) might also cause these diseases."

Absent from that address is any mention of Thimerosal, mercury, or the interaction of them to mitochondria or the immune system.

AAP 2008: "A recent case that went through the federal Vaccine Injury Compensation Program involved a child with a mitochondrial disorder or mitochondrial disease. This case has raised questions about what environmental triggers might bring on or worsen autismlike symptoms in children with such disorders. This case is sealed and details are not public. Mitochondrial cases are extremely rare and should not be used to justify vaccine refusal." 

AAP 2010: "There has been research to suggest that immune responses can influence neurodevelopment and that significant immunologic alterations may play a key pathogenic role in some individuals with ASDs".

AAP 2012: "Despite claims of anti-vaccine proponents who have erroneously linked thimerosal to autism, studies over the past 15 years have not shown evidence of harm. Some of those activists confused ethylmercury with the dangerous neurotoxin methylmercury.

“You’re going to have some people who feel that any amount of mercury in the environment is not a good thing,” said Michael Brady, M.D., FAAP, chair of the AAP Committee on Infectious Diseases. ..... “There is no evidence that suggests the amount of ethylmercury found in thimerosal-containing vaccines is harmful to human health,” the letter read. "  

No evidence?

 Teresa Conrick is Contributing Editor to Age of Autism.