Don't panic. The controversy has been blown WAY out of proportion!
There is no - repeat - NO credible link between mercury and autism.
Most recent studies have found a genetic component in autism.
There is vastly more risk in not vaccinating your child (death, brain damage, etc) than in probability of risk from vaccination. And yes, there is some risk - but in the greater scheme of things the risk is less from being vaccinated than from not being vaccinated.
As far as thimerosal - by all means - ask for the thimerosal free if it makes you feel better, but here is some information that may settle your fears. FYI - some people ARE allergic to thimerosal.
"Thimerosal has been removed from or reduced to trace amounts in all vaccines routinely recommended for children 6 years of age and younger, with the exception of inactivated influenza vaccine (see Table 1). A preservative-free version of the inactivated influenza vaccine (contains trace amounts of thimerosal) is available in limited supply at this time for use in infants, children and pregnant women. Some vaccines such as Td, which is indicated for older children (> 7 years of age) and adults, are also now available in formulations that are free of thimerosal or contain only trace amounts. Vaccines with trace amounts of thimerosal contain 1 microgram or less of mercury per dose.
. . . Thimerosal, which is approximately 50% mercury by weight, has been one of the most widely used preservatives in vaccines. It is metabolized or degraded to ethylmercury and thiosalicylate. Ethylmercury is an organomercurial that should be distinguished from methylmercury, a related substance that has been the focus of considerable study
. . . .Guidelines on Exposure to Organomercurials
Mercury is an element that is dispersed widely around the earth. Most of the mercury in the water, soil, plants and animals is found as inorganic mercury salts. Mercury accumulates in the aquatic food chain, primarily in the form of the methylmercury, an organomercurial. Organic forms of mercury are more easily absorbed when ingested and are less readily eliminated from the body than are inorganic forms of mercury. Humans are exposed to methylmercury primarily from the consumption of seafood (Mahaffey et al. 1997).
. . .One final piece of data regarding thimerosal is worth noting. At the initial National Vaccine Advisory Committee-sponsored meeting on thimerosal in 1999, concerns were expressed that infants may lack the ability to eliminate mercury. More recent NIAID-supported studies at the University of Rochester and National Naval Medical Center in Bethesda, MD examined levels of mercury in blood and other samples from infants who had received routine immunizations with thimerosal-containing vaccines.
Blood levels of mercury did not exceed safety guidelines for methyl mercury for all infants in these studies. Further, mercury was cleared from the blood in infants exposed to thimerosal faster than would be predicted for methyl mercury; infants excreted significant amounts of mercury in stool after thimerosal exposure, thus removing mercury from their bodies. These results suggest that there are differences in the way that thimerosal and methyl mercury are distributed, metabolized, and excreted. Thimerosal appears to be removed from the blood and body more rapidly than methyl mercury. NIAID is sponsoring a follow-up study with larger numbers of infants in Buenos Aires where thimerosal-containing vaccines are still administered to children. See the NIH/NIAID vaccines/thimerosal web site http://www.niaid.nih.gov/factsheets/thimerosalqa.htm. "
http://www.fda.gov/Cber/vaccine/thimerosal.htm#thi
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Also, I've found that if you'll give your son a dose of tylenol about 1/2 hour before the doc actually sees him (usually about the time you get to the office) it really helps stave off crankiness, fever, and swelling.
Warm compresses on the injection site helps, too. Plus lots of rocking and cuddling. :)