The only known side effect of the type of mercury used in some flu shots is mild redness or swelling at the injection site in rare patients who are allergic to it, according to the Centers for Disease Control and Prevention. There are no long-term side effects.
The type of mercury contained in some flu vaccines is part of a preservative called thimerosal, reports the CDC. It is not the same as the naturally occurring mercury known to cause health problems, which is methylmercury. Upon injection into the human body, thimerosal breaks down to form ethylmercury, a different substance. Methylmercury can build up in the body and cause long-term problems, but ethylmercury breaks down quickly and leaves the body.
The FDA removed thimerosal from most childhood vaccines as a precaution, according to the CDC. This was part of a broad effort to remove all types of mercury from a variety of foods and medications, and it was not based on evidence of harm. Although some people claim that thimerosal causes autism, studies have found this to be false.
People who are allergic to thimerosal or who are afraid of side effects can choose other types of flu vaccines, suggests the CDC. Thimerosal is only an ingredient in flu shots that come in multi-dose vials. Most flu vaccines do not contain any thimerosal.