Research on security warnings consistently points to habituation as a key reason why users ignore security warnings. However, because habituation as a mental state is difficult to observe, previous research has examined habituation indirectly by observing its influence on security behaviors. This study addresses this gap by using functional magnetic resonance imaging (fMRI) to open the "black box" of the brain to observe habituation as it develops in response to security warnings. Our results show a dramatic drop in the visual processing centers of the brain after only the second exposure to a warning, with further decreases with subsequent exposures. To combat the problem of habituation, we designed a polymorphic warning that changes its appearance. We show in two separate experiments using fMRI and mouse cursor tracking that our polymorphic warning is substantially more resistant to habituation than conventional warnings. Together, our neurophysiological findings illustrate the considerable influence of human biology on users' habituation to security warnings.