BACKGROUND: Urban American Indian/Alaska Native (AI/AN) adolescents are an understudied population in the USA who are at risk for a variety of health problems. Perceived discrimination (PD), including both overt PD and racial microaggressions (RMA), is known to adversely affect health. However, studies analyzing associations between overt PD and RMA and various health behaviors are limited. METHODS: This study measured past-year alcohol use, heavy drinking, marijuana use, commercialized tobacco use, consequences experienced from alcohol and marijuana use in the past 3 months, mental and physical health status, AI/AN traditional activity participation, and overt PD and RMA among 182 urban AI/AN adolescents in California. To assess the association between overt PD and RMAs and health outcomes, we conducted either logistic regression (for dichotomous outcomes: past-year alcohol use, past-year heavy drinking, past-year marijuana use, consequences of alcohol and marijuana use, commercialized tobacco use) or linear regression (for continuous outcomes: mental and physical health, AI/AN traditional practices). RESULTS: In contrast to our hypotheses, overt PD and RMA were not significantly associated with substance use or mental or physical health among this sample of urban AI/AN adolescents. After adjusting for age and gender, overt PD and RMA were only correlated with past-year cigarette use and alcohol-related consequences experienced in the past 3 months. CONCLUSION: Potential factors that may play a role in decreasing effects of overt PD and RMA among urban AI/AN adolescents are discussed, including participation in AI/AN traditional practices and community engagement.