The majority of cognitive models used in HIV prevention identify risk perception as essential, and the first step towards safer sexual behaviors. Yet, previous studies have rarely examined risk perceptions as an outcome variable, and the few that have, limited their analysis to individual-level determinants. Conspicuously missing in the literature is how school/community level factors affect risk perceptions among school-going youth. Using data collected from primary school youth in Nyanza, Kenya and employing hierarchical linear modeling, this study examines how both individual and community level factors shape individuals' perceived risks of contracting HIV. Results indicate that measures captured at both individual and school/community levels were significantly associated with risk perception. At the individual level, and for boys, high risk perception was associated with higher knowledge about HIV, rejection of myths surrounding HIV transmission, higher condom use self-efficacy and having engaged in risky sexual behaviors. For girls, it was pressure from others to engage in sexual activity, having engaged in risky sexual behaviors and knowing someone infected with HIV that resulted in increased risk perceptions. Beyond individual level variables, some school/community level factors are significantly associated with risk perception. For instance, boys and girls in communities with higher estimates of AIDS deaths reported higher risk perceptions. Boys in communities where AIDS was acknowledged as the cause of death at funerals were less likely to report high risk perceptions. The findings suggest that interventions targeting HIV prevention among young people in Nyanza, Kenya could benefit immensely from an understanding of how schools and communities affect risk perceptions and behavioral change.