Youth living with HIV (YLWH) face significant mental health problems, namely depression, anxiety, and PTSD with rates of these disorders higher than in the general population. This study explored the relationship between symptoms of depression, anxiety, and PTSD and biological markers among a sample of 145 YLWH ages 13–25 years. Participants completed the Center for Epidemiologic Studies Depression Scale (CES-D), Generalized Anxiety Disorder-7 Item Scale (GAD-7), and Primary Care-Posttraumatic Stress Disorder Screen (PC-PTSD). Biological markers included CD4 count and viral load (VL) abstracted from medical records. Findings revealed a relationship between depression and anxiety and CD4 count as well as anxiety and VL. The relationship between depression and anxiety and CD4 count and anxiety and VL was moderated by transmission mode (i.e., behavioral versus perinatal). For youth perinatally infected, greater psychological symptoms of depression and anxiety were associated with a decline in CD4 count and increase in VL, but this was not true for youth with behaviorally acquired HIV. These findings point to the need for individualized mental health prevention and intervention services for YLWH.