The behavioral immune system is considered to be a psychological adaptation that decreases the risk of infection. Research suggests that, in the current environment, this system can produce attitudes with negative health consequences, such as increased vaccine hesitancy. In three studies, we investigated whether two facets of the behavioral immune system—germ aversion (i.e., aversion to potential pathogen transmission) and perceived infectability (i.e., perceived susceptibility to disease)—predicted intentions to accept COVID-19 and influenza vaccination during the pandemic. The behavioral immune system mechanisms were measured before the COVID-19 pandemic in one study, and during the pandemic in two. In contrast to previous research, those with higher germ aversion during the pandemic perceived vaccines to be safer and had higher intentions to accept vaccination. Germ aversion before the pandemic was not associated with vaccination intentions. Individuals who perceived themselves as more susceptible to disease were slightly more willing to accept vaccination. We conjecture that high disease threat reverses the relationship between the behavioral immune system response and vaccination. As the associations were weak, individual differences in germ aversion and perceived infectability are of little practical relevance for vaccine uptake.