The empirical research presented in the article is the realization of a recent project of Sapienza University of Rome, which involved 10 Roman schools (five academic and five technical high schools), including in each of them one section of the 5-year scholastic cycle, for a total sample of 920 students. The aim was to identify contextual, relational and individual factors that activate homophobic prejudice during adolescence. To reduce the atomism and sociological micro-reductionism of survey research, usually used in the study of prejudice, we made use of a methodological approach defined as multilevel and integrated. Besides the role of individual properties (micro level), we examined the combined influence of the processes of collective construction of otherness (macro level) and the properties concerning contexts of socialization and forms of friendship established among adolescents within the schools (meso-social level). The need to link these three levels required the integration of research approaches usually considered as alternatives: sample survey, sociometry and qualitative strategies.