There is no link between prenatal or infant exposure to mercury in vaccines and autism, and "further studies are not warranted," according to the CDC's director of immunization safety.  The researchers looked at the medical records of 256 children with autism and compared them to 256 children without.  They found no significant relationship between the autism cases and the amount of mercury the pregnant mother or baby was exposed to.  The authors took this conclusion as definitive proof that thimerosal, the mercury containing preservative found in season flu vaccines, does not increase the risk of a fetus or infant developing autism.

In 1999 the FDA estimated that infants immunized on the pediatric vaccination schedule were receiving doses of mercury higher than the EPA's recommended intake of mercury in food.  The two chemical formulations of mercury were a single carbon-chain different, but parental and political pressure to remove mercury from vaccines forced most manufacturers to produce a mercury-free version of their shots by 2001.   You'd expect that to decrease rates if autism was related to mercury exposure.  Instead, the opposite happened.

Diagnoses of autism continued to rise, and the majority of vaccination-choice advocates switched from targeting thiomerosal to questioning the number and frequency of vaccinations contained in the schedule itself.  Sixteen shots were given to infants at the time the FDA gave its recommendation in 1999; 25 are recommended before 18 months today (see below schedules).  During the same span of time, the autism rate has tripled from 31 in 10,000 births (California study) to 91 in 10,000 (CDC).

1999 Vaccination Schedule

2010 Vaccination Schedule

Price CS, et al (2010)  "Prenatal and Infant Exposure to Thimerosal From Vaccines and Immunoglobulins and Risk of Autism." Pediatrics. Published online 13 Sept 2010. doi:10.1542/peds.2010-0309.