I will state this up front, I remain unconvinced that the small amounts of thimerosal used in vaccines causes autism, but at the same time I am not ruling out a connection. And I will be perfectly frank in that I believe the refusal to vaccinate on the basis of what amounts to the scientific equivalent of hearsay is the height of parental irresponsibility. At the same time, I am not in favor of mandatory vaccination.
However, if you are worried about thimerosal in vaccines this is a good link for you, John Hopkins compilied a list of common vaccines and their thimerosal levels. It would appear that most contain no thimerosal. Now if you are truly worried still, look at that list and ask the doctor to use one of those on the list and ask them to pull the dose in front of you so you can see the bottle if you are truly paranoid. If they refuse, you can always find a new doc.
This list also brings up something else. A common reason some people are citing for risking their child's health is the thimerosal link to autism. The companies have heard the people's concern and are no longer using it as a preservative, which removes the one objection to vaccinating I could understand. Again, if you are really worried, check the list and don't be afraid to ask. It is a reasonable request to ask the doctor to use a viable alternative and these Thimerosal free vaccines are a reasonable viable alternative.
The other objection, I have heard that companies are pushing vaccines just to make a buck, isn't even worth much of a comment. Do you complain about somebody making some money off the toilet paper you used to wipe your bum?