The paper analyzes the relationships of intergroup tolerance with morality on the basis of the moral foundations theory by J. Haidt. Literature review showed that many researchers view tolerance as an internally inconsistent construct including its moral inconsistency. From the point of view of the moral foundations theory, inconsistency of tolerance may be due to the different relations with individualizing and binding moral foundations: tolerance is consistent with individualizing moral foundations (autonomy ethics) and inconsistent with binding moral foundations (community ethics). Such inconsistency has to manifest itself in the case of tolerance towards potentially dangerous groups. This hypothesis was tested in our study, which included 202 university students aged 18-46 (36% males). They answered the questions of “Moral foundations questionnaire” (MFQ by Graham) and “Multifactor inventory of tolerance” (MIT by Babaeva & Sabadosh). Using exploratory factor analysis, we discovered two types of groups: derogated (elder, sick, marginal people, and opposite sex) and dangerous groups (people of different religiosity, nationality, criminals, and strangers). To test the hypothesis we constructed the structural model, where the autonomy ethics was positively correlated with tolerance towards derogated and dangerous groups, while community ethics was negatively correlated with tolerance towards dangerous groups. Good fit of this model to our data lets us to conclude that autonomy ethics is consistent with tolerance towards any group while community ethics is inconsistent with tolerance towards dangerous groups. These correlations between tolerance and moral foundations discover the fundamental inconsistency of tolerance in the context of autonomy and community ethics.