What is thimerosal?

Thimerosal is a preservative that was used in some multi-use vials of vaccine.  Thimerosal contains 49% mercury which is a known neurotoxin and nephrotoxin (poison to the brain and kidneys).  There was a debate about whether the amount of mercury children were exposed to via thimerosal in vaccines was enough to cause any damage.  Since the true "safe" level of mercury is not known, thimerosal has been removed from vaccines manufactured in the US since 2001. 

Why was thimerosal added to vaccines?

Multi-use vials of vaccine require preservatives in order to suppress the growth of unwanted agents such as bacteria.  Thimerosal was often selected over other preservatives because it worked very well as a preservative and it was relatively inexpensive.

Difficulty in determining the safe level of mercury:

Although it is know that too much mercury caused problems, it is difficult to determine what a safe level of mercury exposure may be.  It is obviously immoral to do experiments where children are intentionally exposed to mercury to determine whether or not they show symptoms.  For this reason, different agencies have different calculations for determining what they consider a safe level.  Most of these calculations include much bias on the side if safety: for example assuming a small child receiving maximum number of doses plus a safety margin to account for possible human variation.  It is assumed that infants respond to mercury in the same way as fetuses do in utero, while in reality fetuses are almost certainly more susceptible to neurotoxins such as mercury. Most of the available data is for methylmercury, while the breakdown product of thimerosal is the more rapidly metabolized ethylmercury.  Because of all these reasons, an accurate safe level of thimerosal exposure is unknown.

Decision to remove thimerosal:

Although it was never proven that the level of mercury exposure form thimerosal in vaccines caused problems, developmentally or otherwise, the committee could also not prove that such exposure was entirely safe.  Furthermore, a suitable alternative was available.  To err on the safe side, the decision was made in the US, to remove thimerosal from vaccines for children.  Because of the lack of preservative, many vaccines are now distributed in single use vials and need constant refrigeration to suppress unwanted bacterial growth.

Links:

Vaccines: Vaccinations and Mercury

Immunization Safety Review: Thimerosal