Alcohol affects the transmission and treatment of HIV, yet may be under-reported in resource-limited settings. We compared self-reported alcohol consumption with levels of plasma carbohydrate-deficient transferrin (%CDT), a biomarker of heavy alcohol consumption, in persons initiating antiretroviral therapy in Uganda. Almost seven percent (6.7%) of persons reporting abstaining and 10% reporting consuming 1-40 drinks in the prior month tested positive for %CDT, and actual under-report may be higher due to low sensitivity of %CDT. These results suggest likely under-report in those reporting abstaining and current drinking. Improved identification of heavy alcohol consumption is needed for research and clinical purposes.