Previous research, over a decade old, suggests students attending alternative high schools (AHS) engage in high levels of health-risk behaviors. Data from the 2007 Minnesota Student Survey for students attending AHS (n = 2,847) and traditional high schools (THS; n = 87,468) were used for this cross-sectional analysis to compare prevalence estimates, adjusted for age, race/ethnicity, and free and reduced lunch, for 28 health-risk behaviors. Students attending AHS were significantly more likely than students attending THS to report engaging in all behaviors related to unintentional injury and violence, tobacco use, alcohol and other drug use, and sexual activity, and were significantly less likely to report participating in physical activity, including sports teams. Students attending AHS continue to engage in high levels of health-risk behaviors as compared to their peers in THS. Updated national prevalence data were needed, as well as studies examining the role of protective factors in the lives of students attending AHS.