Background: The aim of the present study was to analyze the association between course type and health among high school students. Methods: A cross-sectional study with 675 Brazilian high school students. The independent variable was course type (general or vocational) and dependent variables were health characteristics. All information was obtained by a self-report questionnaire and the following health characteristics were analyzed: mental health, physical activity, sedentary behavior, food consumption, daytime sleepiness, tobacco use, alcohol consumption, aggression, and musculoskeletal symptoms. The prevalence ratio (PR) was estimated by Poisson regression. Results: Vocational students presented a higher prevalence in 7 of the 20 mental health symptoms analyzed (PR = 1.21-1.64), daytime sleepiness (PR = 1.39-1.71), and musculoskeletal symptoms in neck, shoulders, low back, and knees (PR = 1.31-1.41), and a lower likelihood of being physically active (PR = 0.59-0.70). Conversely, vocational students showed lower sedentary behavior on TV and videogames during the week (PR = 0.35-0.46), consumption of snacks, cookies, and crackers (PR = 0.56-0.72), and experiences of aggression (PR = 0.13-0.17), all P < 0.05. Conclusions: High school can affect students' health distinctly, indicating that intervention programs and health monitoring should be specific to course type.