No, the vaccines generally don't have mercury in them, especially if the vaccinations come from "single dose vials." The mercury (thimerosol) was used as a preservative in multi-dose vials, but these have been largely phased out, with the possible exception of influenza vaccine.
Further, there is no proof, and this area has been extensively studies, that the amount of mercury was enough to hurt children. (Remember, even us physicians have our own children who we vaccinate.) But to make the public more confident, the vaccines were changed so as to remove even this tiny amount of mercury.
Of course, all medications have potential side effects. But on balance, the benefits of the vaccines greatly outweigh any potential side effects.
A great story to tell is that of the first generation vaccine for rotavirus, a virus which causes dehydration and hospitalization. Even though it was tested in 10s of thousands of children before licensure and release, it was found about one year after being used that a rare but definite side effect, intussusception (telescoping of the intestines) was due to the vaccine. The vaccine was withdrawn from the market, causing the drug manufacturer to lose about $250 million.
And better, a new generation of the vaccine (about six years later) has been released, after very extensive evaluation for the same problem, which apparently doesn't occur with this.
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