OBJECTIVES: Mental illness and substance abuse have been consistently associated with poor HIV-medication adherence and other negative health outcomes. METHODS: A brief mental health and substance use screening instrument was administered to 1,362 HIV-infected individuals receiving care at two academic medical center Infectious Diseases Clinics in North Carolina. RESULTS: Study results indicated high frequencies of symptoms of mental illness (60%), substance abuse (32%), and co-occurring symptoms of mental illness and substance abuse (23%). Younger age (P = 0.03), male sex (P < 0.001), and higher viral load (P < 0.001) were associated with substance use problems. White race (P = 0.001), younger age (P = 0.023), and higher viral load (P = 0.042) were associated with symptoms of mental illness. CONCLUSIONS: In the Southeast, mental health and substance abuse services are sparse and stigma is high; thus, innovative treatment strategies are needed to address the high levels of co-occurring mental illness and substance abuse. Antiretroviral therapies will not reach their potential for slowing the HIV/AIDS epidemic and prolonging survival if comorbidities that influence patient behavior are not addressed.