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 < .05. CONCLUSIONS High school can affect students' health distinctly, indicating that intervention programs and health monitoring should be specific to course type.