Aims To determine alcohol use effect on HIV treatment success and whether alcohol use mediates the relation between male sex and treatment failure. Design Longitudinal cohort study. Setting Eight HIV clinics in and near Gaborone, Botswana. Participants A total of 938 HIV-infected treatment-naive adults initiating regimens containing the antiretroviral medication efavirenz between June 2009 and February 2013, including 478 (51%) males, median age 38 years, and plasma HIV RNA 4.9 log10 copies/ml. Measurements Primary outcome was a composite of treatment failure over 6 months including death, lost to care or plasma HIV RNA > 25 copies/ml. Exposures included alcohol use and gender. Findings Failure in 339 (36%) participants included 40 (4%) deaths, 194 (21%) lost to care and 105 (11%) with HIV RNA > 25 copies/ml. Both hazardous alcohol use in the past year [adjusted odds ratio (aOR) = 1.4, 95% confidence interval (CI) = 1.0, 1.9] and male sex (aOR = 2.1, 95% CI = 1.5, 2.9) were associated with failure. Hazardous alcohol use in the year prior to enrollment was more common in men (57%) than women (24%), P < 0.001. There was no difference in alcohol use effect on failure between sexes (P for interaction > 0.5). Controlling for hazardous alcohol use did not change the relation between sex and failure. Conclusion Alcohol use among HIV-infected adults in Botswana appears to worsen HIV treatment outcomes. Alcohol use does not appear to have either a mediating or a moderating effect on the relation between gender and HIV treatment outcome failure.