Here is a review that has taken into account pharmacokinetic and epidemiologic studies published between 2003 and 2008 and failed to prove a cause-effect relationship between thimerosal containing vaccines (TCV) and autism:
Although immunization provides important benefits to public health, associated risks are inevitable. However, studies have consistently failed to identify a cause-effect relationship between thimerosal and autism. In addition, the prevalence of autism has increased despite a decrease in the thimerosal content of vaccines; this finding further suggests that there is not an association between thimerosal and autism but that the increased prevalence of autism may be attributable to improved diagnostic criteria and increased awareness of autism. Despite failure to demonstrate an association, certain states continue to mandate that vaccines given to children contain no more than trace amounts of thimerosal.
Epidemiologic studies continue to provide evidence that there is no association between thimerosal exposure and autism. Whereas an infant younger than 6 months in 1999 could have been exposed to approximately 200 mcg of mercury derived from vaccines, the current amount is less than 3 mcg, if certain influenza vaccines are not included. Children should receive recommended immunizations to prevent serious disease. The known risks of serious complications from preventable infections—e.g., influenza—outweigh the risks of adverse consequences from vaccines, including thimerosal containing vaccines.
Source: Anne M. Hurley, PharmD, Mina Tadrous, PharmD, MS, and Elizabeth S. Miller, PharmD. Thimerosal-Containing Vaccines and Autism: A Review of Recent Epidemiologic Studies. J Pediatr Pharmacol Ther. 2010 Jul-Sep; 15(3): 173–181.
This eighth and final report of the Immunization Safety Review Committee examines the hypothesis that vaccines, specifically the measles-mumps-rubella (MMR) vaccine and thimerosal-containing vaccines, are causally associated with autism. The committee reviewed the extant published and unpublished epidemiological studies regarding causality and studies of potential biologic mechanisms by which these immunizations might cause autism. The committee concludes that the body of epidemiological evidence favors rejection of a causal relationship between the MMR vaccine and autism. The committee also concludes that the body of epidemiological evidence favors rejection of a causal relationship between thimerosal-containing vaccines and autism. The committee further finds that potential biological mechanisms for vaccine-induced autism that have been generated to date are theoretical only.
Source: Institute of Medicine (US) Immunization Safety Review Committee. Immunization Safety Review: Vaccines and Autism. Washington (DC): National Academies Press (US); 2004. Available from: http://www.ncbi.nlm.nih.gov/books/NBK25344/
Here is a study conducted in Poland that concludes the same:
Conditional logistic regression was used to assess the risk of autism due to TCVs exposure. No significant association was found between TCVs exposure and autism. After adjusting to potential confounders, odds ratios of the risk of autism developing for infants vaccinated with TCVs were 1.52 (95% CI: 0.29-11.11) for doses 12.5-87.5 microg, 2.78 (95% CI: 0.29-11.11) for 100-137.5 microg and 1.97 (95% CI: 0.37-18.95) for these exposed > or = 150 microg. Our study revealed no evidence of an association between TCVs and autism.
Source: Mrozek-Budzyn D, Majewska R, Kiełtyka A, Augustyniak M. [Lack of association between thimerosal-containing vaccines and autism]. Przegl Epidemiol. 2011;65(3):491-5. PubMed PMID: 22184954.
So, how did thimerosal get associated with autism? Well, it seems to be neurotoxic on cell cultures when glutathione levels are low (low glutathione is a common situation in autism):
Because mercury has a high affinity for thiol (sulfhydryl (-SH)) groups, the thiol-containing antioxidant, glutathione (GSH), provides the major intracellular defense against mercury-induced neurotoxicity. Cultured neuroblastoma cells were found to have lower levels of GSH and increased sensitivity to thimerosol toxicity compared to glioblastoma cells that have higher basal levels of intracellular GSH. Thimerosal-induced cytotoxicity was associated with depletion of intracellular GSH in both cell lines.
Source: James SJ, Slikker W, Melnyk S, New E, Pogribna M, Jernigan S. Thimerosal neurotoxicity is associated with glutathione depletion: protection with glutathione precursors. Neurotoxicology. 2005 Jan;26(1):1-8. doi: 10.1016/j.neuro.2004.07.012. PubMed PMID: 15527868.