Background: Substance use and poor dietary practices are prevalent among adolescents. The purpose of this study was to examine frequency of substance use and associations between cigarette, alcohol and marijuana use and selected dietary practices, such as sugar-sweetened beverages, high-fat foods, fruits and vegetables, and frequency of fast food restaurant use among alternative high school students. Associations between multi-substance use and the same dietary practices were also examined. Methods. A convenience sample of adolescents (n = 145; 61% minority, 52% male) attending six alternative high schools in the St Paul/Minneapolis metropolitan area completed baseline surveys. Students were participants in the Team COOL (Controlling Overweight and Obesity for Life) pilot study, a group randomized obesity prevention pilot trial. Mixed model multivariate analyses procedures were used to assess associations of interest. Results: Daily cigarette smoking was reported by 36% of students. Cigarette smoking was positively associated with consumption of regular soda (p = 0.019), high-fat foods (p = 0.037), and fast food restaurant use (p = 0.002). Alcohol (p = 0.005) and marijuana use (p = 0.035) were positively associated with high-fat food intake. With increasing numbers of substances, a positive trend was observed in high-fat food intake (p = 0.0003). There were no significant associations between substance use and fruit and vegetable intake. Conclusions: Alternative high school students who use individual substances as well as multiple substances may be at high risk of unhealthful dietary practices. Comprehensive health interventions in alternative high schools have the potential of reducing health-compromising behaviors that are prevalent among this group of students. This study adds to the limited research examining substance use and diet among at-risk youth. Trial registration number. ClinicalTrials.gov: NCT01315743.