PurposeAlternative high schools (AHS) are designed to provide individualized education, more flexible scheduling, and smaller class sizes for students referred out of traditional high school. AHS students report higher levels of substance use (SU) and face disproportionately higher levels of trauma and toxic stress than their traditional high school peers. We sought to examine whether generational immigration (GenIm) status modifies the association of mental health and SU among AHS students using a longitudinal study of 1,060 Southern California AHS students. MethodsSubscales from the 21-item Depression Anxiety Stress Scale were administered. Effect modification was examined by GenIm status defined as first generation (born outside of the United States), second generation (born in the United States with a parent born outside the United States), or third generation (born in the United States with US-born parent(s)). Main outcomes included the number of times different substances were used in the past year over a 3-year period. ResultsMultilevel, negative binomial, covariate-adjusted latent growth curve models generated incidence rate ratios (IRRs) and 95% confidence intervals (CIs) of the time-varying association between depression, anxiety, or stress and the use of cigarettes, e-cigarettes, cigars, alcohol, or marijuana. Multiple-group models examined effect modification by GenIm status. DiscussionThe link between mental health and SU was stronger among first- and second-generation students than third-generation students. For example, a one-unit increase in stress relative to the average stress of students from the same school was associated with an increase in the rate of e-cigarette use among first-generation (IRR = 2.03, 95% CI = 1.07–3.85), second-generation (IRR = 2.25, 95% CI = 1.86–2.72), and third-generation (IRR = 1.68, 95% CI = 1.31–2.16) students. Effective strategies tailored to subgroups of AHS students are needed to counter disparities between traditional and alternative school systems that may contribute to long-term trajectories of SU.