Background: The prevention and intervention of adolescent substance use is a public health priority. Most adolescents will engage in some form of substance use, and a sizeable minority will transition to using multiple substances. An emerging body of research takes a person-centered approach to model adolescent substance use over time; however, the findings have been equivocal. Our study modeled adolescent substance use transition patterns over three years based on a comprehensive list of substances and examined gender as a moderator. Methods: We used three annual waves of data (Time 2, Time 3, and Time 4) from an ongoing longitudinal study of an ethnically diverse sample of 1042 adolescents originally recruited from multiple high schools in southeast Texas. Participants were 56% female, 32% Hispanics, 30% Whites, 29% African Americans, and 9% other with an average of 16.1 years (SD = 0.79) at Time 2. Data were analyzed using latent transition analyses. Results: The study identified three substance use statuses (Mild Alcohol Use, Alcohol and Moderate Marijuana Use, and Polysubstance Use) and suggested that adolescents generally remained in the same statuses over time. When they did transition, it was typically to a more harmful substance use status. Further, males were more likely than females to be polysubstance users and had higher probabilities of transiting to and remaining in a more harmful drug use status. Conclusions: The study identifies overall and gender specific adolescent substance use transition patterns, which are vital to informing intervention development.