As the pediatric HIV epidemic in resource-rich countries evolves into an adolescent epidemic, there is a substantive need for studies elucidating mental health needs of perinatally HIV-infected (PHIV + ) youth as they transition through adolescence. This article examines the role of perinatal HIV infection in influencing mental health by comparing the changes in psychiatric disorders and substance use disorders (SUD) in PHIV + and perinatally HIV-exposed, but uninfected (PHIV − ) youth over time. Participants were recruited from four medical centers in New York City. Individual interviews were administered at baseline and 18-month follow-up to 166 PHIV + and 114 PHIV– youth (49% male, age 9–16 years at baseline). Youth psychiatric disorder was assessed using the caregiver and youth versions of the Diagnostic Interview Schedule for Children (DISC-IV). Over two-thirds of participants met criteria for at least one psychiatric disorder at either baseline or follow-up, with few group differences. Among PHIV + youth, there was a significant decrease in the prevalence of any psychiatric disorder, as well as anxiety disorders specifically over time, whereas the prevalence of any psychiatric disorder among PHIV– youth remained the same and mood disorders increased. Rates of SUD were low in both groups, increasing slightly by follow-up. PHIV + youth reported more use of mental health services at follow-up. CD4 count and HIV RNA viral load were not associated with the presence or absence of disorder at either time point. In conclusion, among PHIV + and PHIV− youth, the rates of psychiatric disorder were high, even compared to other vulnerable populations, suggesting that factors other than perinatal HIV infection may be important determinants of mental health. PHIV + youth were more likely to improve over the observation period. The data underscore the critical need for mental health interventions for both PHIV + and PHIV− youth.