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Objective To examine the longitudinal association between sexual behavior and substance use in perinatally HIV-infected (PHIV+) and perinatally HIV-exposed-but-uninfected (PHIV−) youth. Methods Growth curve modeling was used with data from N = 340 PHIV-exposed youth (60.6% PHIV+; 9–22 years) to estimate the onset of penetrative and unprotected sex across time, adding alcohol and marijuana use trajectories as time-varying covariates and examining HIV-status differences. Results The odds of penetrative or unprotected sex more than doubled across time. Alcohol and marijuana use significantly increased the odds of engaging in sex and unprotected sex, with no HIV-status differences. The association between unprotected sex and alcohol use was less salient for PHIV+ than PHIV− youth. Conclusions Similar to youth from other populations, PHIV+ and PHIV− youth are increasingly engaging in sex and substance use as they age. Targeted interventions to prevent sexual risk behavior and further HIV transmission should address the influence of substance use.