There is substantial evidence that intolerance arises from perceptions of difference. A prevailing view holds that even if intolerance is understandable as a defense mechanism, or as an attitude intended to ward off threatening groups and noxious activities, it often is the result of human irrationality and indulgence of prejudice. This conclusion is supported by studies that seem to demonstrate the apparent irrelevance of the actual level of threat to levels of intolerance. These studies show human actions attendant to diversity are caused by established convictions (i.e., prejudice) rather than by the degree of threat. However, informed by theoretical approaches provided by neuroscientists, we report findings that threat is, indeed, a provocative factor that modifies political tolerance in predictable ways. Previous studies defined threat as probabilistic assessments of the likelihood of bad events. When threat is defined as novelty and normative violations (i.e., as departures from expected, or normal, occurrence), then consistent relationships to intolerance are obtained.