Background: The purpose of this study was to examine 1) the prevalence of psychiatric and substance use disorders in perinatally HIV-infected (HIV+) adolescents and 2) the association between HIV infection and these mental health outcomes by comparing HIV+ youths to HIV exposed but uninfected youths (HIV-) from similar communities. Methods: Data for this paper come from the baseline interview of a longitudinal study of mental health outcomes in 9-16 year old perinatally HIV-exposed youths (61% HIV+) and their caregivers. Three hundred forty youths and their primary adult caregivers were recruited from four medical centers and participated in separate individual interviews. Youth psychiatric disorder was assessed using the caregiver and youth versions of The Diagnostic Interview Schedule for Children (DISC-IV). Results: According to caregiver or youth report, a high percentage of HIV+ and HIV- youths met criteria for a non-substance use psychiatric disorder, with significantly higher rates among the HIV+ youths (61% vs. 49%, OR = 1.59; CI = 1.03,2.47; p less than 0.05). The most prevalent diagnoses in both groups were anxiety disorders (46% for total sample) which included social phobia, separation anxiety, agoraphobia, generalized anxiety disorder, panic disorder, obsessive-compulsive disorder, and specific phobias. One quarter of the sample met criteria for a behavioral disorder (ADHD, conduct disorders, and oppositional defiant disorders), with ADHD being most prevalent. HIV+ youths had significantly higher rates of ADHD (OR = 2.45; CI = 1.20, 4.99, p less than 0.05). Only 7% of youths met criteria for a mood disorder and 4% for a substance abuse disorder. Several caregiver variables (caregiver type and HIV status) were also associated with both child HIV status and mental health outcomes. Conclusions: Our data suggest that HIV+ youths are at high risk for mental health disorders. Further longitudinal research is necessary to understand the etiology, as well as potential protective factors, in order to inform efficacy-based interventions.