Perceived stress—an endophenotype indicative of the tendency to appraise stress as frequent, unpredictable and unmanageable—is associated with adolescent cigarette smoking. It is unclear whether this association: (1) extends to alternative tobacco products, like electronic cigarettes and hookah (tobacco water pipe), which are increasingly popular among youth, and (2) differs by gender. In this report, data were drawn from a population-based longitudinal cohort of youth in Southern California. Perceived stress was assessed at baseline (7th or 8th grade; 2010). Electronic cigarette, hookah, combustible cigarette, and cigar use were assessed at a 4-year follow-up (11th or 12th grade; 2014). After adjusting for confounders, polytomous logistic regressions showed that a standardized baseline perceived stress score (M=0, SD=1) predicted electronic cigarette, hookah, combustible cigarette, and cigar use and a poly-tobacco use index at the 4-year follow-up in the overall sample. Interactions between perceived stress and gender were also observed (Interaction Ps<.05), which demonstrated that the association of perceived stress with tobacco product use and poly-use were stronger in females (ORs for current use range: 1.47 to 1.72) than males (ORs range: 0.93 to 1.31). Adjusting for baseline perceived stress, the change in perceived stress from baseline to follow-up was also positively associated with use and poly-use of most tobacco products in females and in males to some extent. In the current era in which teen use of alternative tobacco products is increasingly common, adolescent tobacco use and poly-use research and prevention strategies should address gender-specific origins of tobacco product use risk and consider perceived stress and other emotional endophenotypes in such risk pathways.