Substance use complicates HIV care and prevention. Primary care clinics are an ideal setting to screen for and offer interventions for unhealthy alcohol and drug use; however, few HIV clinics routinely screen for substance use. We enrolled 208 clinic patients at an urban underserved HIV primary care clinic. We screened the patients for substance use with the Alcohol, Smoking, and Substance Involvement Score Test and measured urine toxicology. Of the 168 participants who completed screening, the majority reported tobacco or nonprescribed substance use in the previous 3 months. More African American participants reported low or no risk amphetamine use compared to Hispanic, White, or Other race participants (p < .001). Implementing standard clinic practice for screening and assessing substance use in HIV primary care clinics is needed.