In this article, we suggest that dogmatic beliefs, manifested as strong beliefs that there is no God (i.e., dogmatic atheism) as well as strong beliefs in God (i.e., religious orthodoxy), can serve as a cognitive response to uncertainty. Moreover, we claim that people who dogmatically do not believe in religion and those who dogmatically believe in religion are equally prone to intolerance and prejudice towards groups that violate their important values. That is because prejudice towards these groups may be an efficient strategy to protect the certainty that strong beliefs provide. We tested these assumptions in two studies. In Study 1 and Study 2, we demonstrated that dogmatic beliefs mediate the relationship between intolerance to uncertainty and both, religious orthodoxy and dogmatic atheism. In addition, in Study 2 we showed that both the religiously orthodox and dogmatic atheists become prejudiced towards groups that violate their values and that these effects are especially strong under experimentally induced uncertainty. In this study, we focused on atheists and homosexuals as groups that pose a threat to Christian’s religious worldviews, and Catholics and pro-life supporters as groups that pose a threat to the values of atheists. The results are discussed in relation to past research on dogmatism and religion, as well as with reference to what this means for the study of prejudice