The main goal of this paper is to analyze the connection between confidence in institutions and the (dis)integration of multiethnic communities in Croatia. The paper consists of two parts. The first discusses the importance of analytical distinction between social and system integration. It comprises a brief overview of empirical studies that have analyzed the processes of (dis)integration of multiethnic communities by comparing cities and municipalities where ethnic conflicts occurred (conflict areas) and those in which they did not (peace areas). The second part, based on data collected by the questionnaire method, studies the differences in confidence in institutions between multiethnic areas of peace and conflict. The paper also attempts to establish the extent to which these phenomena have been determined by value orientations, political views and the respondents’ level of education. The results indicate that there are differences between the areas analyzed. The respondents from the conflict areas show a higher degree of confidence in social institutions than the respondents from peace areas. The results also indicate that confidence in institutions in those areas is not based on equal social and cultural grounds. In peace areas, it is based on acceptance of the values of Europeism, rejection of social pessimism and the respondents’ level of education. Meanwhile, in conflict areas, in addition to the aforementioned factors, the nationalistic value system rooted in acceptance of ethnocentrism and the right-wing political orientation also plays a vital role.