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The cultural roles and expectations attributed to individuals based on their sex often shape health behaviors and outcomes. Gender nonconformity (GNC) (ie, gender expression that differs from societal expectations for feminine or masculine appearance and behavior) is an underresearched area of adolescent health that is often linked to negative health outcomes.To examine the associations of GNC with mental distress and substance use among high school students.Cross-sectional study based on data from the Youth Risk Behavior Survey (YRBS) conducted in 2015. The setting was 3 large urban US school districts (2 in California and 1 in Florida). Participants were a racially/ethnically diverse population-based sample of 6082 high school students representative of all public school students in grades 9 through 12 attending these 3 school districts.Sex-stratified adjusted prevalence ratios (APRs) (adjusted for race/ethnicity, grade, and sexual identity) for high gender-nonconforming students (very/mostly/somewhat feminine male students or very/mostly/somewhat masculine female students) and moderate gender-nonconforming students (equally feminine and masculine students) relative to a referent group of low gender-nonconforming students (very/mostly/somewhat masculine male students or very/mostly/somewhat feminine female students).Among 6082 high school students, 881 (15.9%) were white, 891 (19.1%) black, 3163 (55.1%) Hispanic, and 1008 (9.9%) other race/ethnicity. Among female students (2919 [50.0% of the study population]), moderate GNC was significantly associated with feeling sad and hopeless (APR, 1.22; 95% CI, 1.05-1.41), seriously considering attempting suicide (APR, 1.41; 95% CI, 1.14-1.74), and making a suicide plan (APR, 1.52; 95% CI, 1.22-1.89); however, substance use was not associated with GNC. Among male students (3139 [50.0% of the study population]), moderate GNC was associated with feeling sad and hopeless (APR, 1.55; 95% CI, 1.25-1.92); high GNC was associated with seriously considering attempting suicide (APR, 1.72; 95% CI, 1.16-2.56), making a suicide plan (APR, 1.79; 95% CI, 1.17-2.73), and attempting suicide (APR, 2.78; 95% CI, 1.75-4.40), as well as nonmedical use of prescription drugs (APR, 1.81; 95% CI, 1.23-2.67), cocaine use (APR, 2.84; 95% CI, 1.80-4.47), methamphetamine use (APR, 4.52; 95% CI, 2.68-7.61), heroin use (APR, 4.59; 95% CI, 2.48-8.47), and injection drug use (APR, 8.05; 95% CI, 4.41-14.70).This study suggests mental distress is associated with GNC among female and male students. Substance use also appeared to be strongly associated with GNC among male students. These findings underscore and suggest the importance of implementing school-based programs to prevent substance use and promote student mental health that are inclusive of gender diversity in students.