Flu shots have raised similar alarms in young children. In the 2011 flu season, the U.S. Food and Drug Administration confirmed 42 cases of seizures, 36 of them involving infants and 10 of them deemed "serious," after vaccination with Fluzone, a vaccine made by Sanofi-Pasteur.

The CDC's decision to play up flu deaths dates back a decade, when it realized the public wasn't following its advice on the flu vaccine. During the 2003 flu season "the manufacturers were telling us that they weren't receiving a lot of orders for vaccine,"Dr. Glen Nowak, associate director for communications at CDC's National Immunization Program, told National Public Radio.