Alcohol use may have a negative impact on the course of HIV disease and the effectiveness of its treatment. We studied patients with HIV who use alcohol and associated socio-demographic, health and psychosocial factors. Outcomes from this study may help in selecting patients from clinical practice with high-risk alcohol use and who are likely to benefit most from alcohol reduction interventions. In a cross sectional study in three primary health care clinics in Pretoria, South Africa, from January 2012 to June 2012, patients with HIV infection were interviewed and patients' medical files were reviewed to obtain data on levels of alcohol use (Alcohol Use Disorder Identification Test), patients' socio-demographic characteristics, HIV-related information, health related quality of life (WHOQoL-HIVBref), internalized AIDS stigma, symptoms of depression and adherence to antiretroviral therapy. Analyses consisted of descriptive statistics, bi- and multivariate logistic regression models. A total of 2230 patients (1483 [66.5%] female) were included. The median age was 37 years (interquartile range 31-43), 99.5% were black Africans, 1975 (88.6%) had started ART and the median time on ART was 22 months (interquartile range 9-40). No alcohol was used by 64% of patients, 8.9% were low risk drinkers, 25.1% of patients were hazardous or harmful drinkers and 2.0% had possible alcohol dependence. In multivariate analysis high-risk drinking was positively associated with male gender, never being married, tobacco use, a higher score for the level of independence'-domain measured with the WHOQoL-HIVBref questionnaire, and with more depressive symptoms compared to low-risk drinking. This study shows a high prevalence of hazardous or harmful drinking in patients with HIV infection (especially men) attending primary health care clinics in South Africa. Routine screening for alcohol use should be introduced in these clinics and harm reduction interventions should be evaluated, taking into account associated factors.