HIV has become a highly treatable disease due to advances in antiretroviral therapy (ART). Additionally, HIV-infected individuals often take opiates, barbiturates, and benzodiazepines to treat co-occurring conditions, including pain and symptoms of HIV. We sought to examine prescription medication misuse by surveying 295 HIV-infected patients receiving ART. Participants answered questions about their demographics, alcohol and other drug use, psychiatric diagnoses, ART adherence and side effects, and quality of life. Eleven percent of our sample acknowledged prescription medication misuse. In regression analysis, prescription medication misusers were more likely to report any drinking to intoxication (OR=4.31, 95% CI: 1.35-13.76, p=0.013), reported greater severity of ART side effects (OR=1.05, 95% CI: 1.01-1.10, p=0.041), and demonstrated poorer cognitive functioning (OR=0.97, 95% CI: 0.94-0.99, p=0.048) compared to those who did not misuse prescription medications. Special care should be taken by medical providers before prescribing medications that may be abused or diverted. Patients should also be screened for aberrant use, even if not prescribed. ART side effects, cognitive deficits, and alcohol abuse may serve as risk factors or indicators of prescription medication misuse, and should be monitored.