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Thimerosal is a preservative used in vaccines to prevent spoiling, to inactivate bacteria used to make certain vaccines, and to prevent bacterial contamination in the finished vaccine. Several reports have linked the thimerosal in vaccines to mercury poisoning because thimerosal contains a mercury related compound. Since infants receive many vaccines, the reports have pointed to the mercury poisoning from thimerosal containing vaccines as a possible cause of autism. Mercury can cause immune, sensory, neurological, motor, and behavioral dysfunctions. The FDA is working towards eliminating or reducing the amount of thimerosal in vaccines.

Thimerosal is a preservative that has been used in some vaccines since the 1930's, when it was first introduced by Eli Lilly Company. It is 49.6% mercury by weight and is metabolized or degraded into ethyl mercury and thiosalicylate. At concentrations found in vaccines, it meets the requirements for a preservative as set forth by the United States Pharmacopeia; that is, it kills the specified challenge organisms and is able to prevent the growth of the challenge fungi. Prior to its introduction in the 1930's, data were available in several animal species and humans providing evidence for its safety and effectiveness as a preservative. Since then, thimerosal has a long record of safe and effective use preventing bacterial and fungal contamination of vaccines, with no ill effects established other than minor local reactions at the site of injection.

While the use of mercury-containing preservatives has declined in recent years with the development of new products formulated with alternative or no preservatives, thimerosal is still used in certain antivenins, skin test antigens, and ophthalmic and nasal products, in addition to certain vaccines recommended for adults or older children. As a vaccine preservative it is used in concentrations of 0.003% to 0.01%. A vaccine containing 0.01% thimerosal as a preservative contains 50 micrograms of thimerosal per 0.5 ml dose or approximately 25 micrograms of mercury per 0.5 mL dose.

An association that has been noted by some concerned parents of autistic children is that the increase in the prevalence of autism over the last few decades "closely matches the introduction and spread of thimerosal-containing vaccines". This type of comparison is known as an ecological study. Ecological studies alone are generally not accepted as strong evidence of causality, because they do not link individual exposure to individual outcome, and can be subject to confounding by unknown or uncontrollable factors. In addition, it has been noted that some children with autism have high levels of mercury in hair, urine and blood. This observation cannot be interpreted without information on the levels of mercury in individuals without autism (i.e. case-control study). However, such observations do indicate that the hypothesis should be studied further.