Objective: Assess the mental health and substance use of sexual minority collegiate student-athletes in the United States, as compared with heterosexual college students and heterosexual student-athletes. Participants: Undergraduate students (N = 196,872) who completed the American College Health Association's National College Health Assessment (Fall 2008-Fall 2012 administrations). Methods: Written cross-sectional survey. Results: Sexual minority student-athletes had a higher risk of experiencing mental health difficulties than their heterosexual athlete peers. There were no significant differences in mental health between sexual minority male athletes and nonathletes. Sexual minority female athletes appeared to fare better than nonathlete peers. Substance use was greater among sexual minority students (athlete and nonathlete) and was mediated by mental health. Conclusions: Participation in athletics does not appear to be associated with an elevated risk of negative mental health outcomes for sexual minority participants; however, there are disparities in mental health outcomes by sexual orientation regardless of athletics participation.