BACKGROUND: Uganda has one of the highest per capita alcohol consumption rates in sub-Saharan Africa. However, the prevalence of alcohol use disorders (AUD) remains unknown in many areas, especially in rural districts. This study aimed to estimate the prevalence of alcohol consumption and of alcohol use disorder among men, and to describe the distribution of drinking intensity, among men in in Kamuli District, Uganda. METHODS: Men attending primary care clinics in Kamuli District were consecutively interviewed in a facility-based cross-sectional study, and a separate group of men were interviewed in a population-based cross-sectional study. In both studies the men were administered a structured questionnaire, which included the alcohol use disorder identification test (AUDIT) to screen for AUD, as well as sections about demographic characteristics, depression screening, internalized stigma for alcohol problems and treatment-seeking. RESULTS: Among the 351 men enrolled in the Community study, 21.8% consumed alcohol in the past 12 months, compared to 39.6% of 778 men in the Facility Survey. The proportion of men who screened positive for AUD was 4.1% in the community study and 5.8% in the facility study. AUDIT scores were higher among older men, men with paid/self-employment status and higher PHQ-9 score (P < 0.05). Nearly half (47.5%) of the men with AUDIT-positive scores reported that alcohol use problems had ruined their lives. A majority (55.0%) of men with AUDIT-positive scores did not seek treatment because they did not think AUD was a problem that could be treated. CONCLUSIONS: Internalized stigma beliefs among AUDIT-positive men impede treatment-seeking. As part of any efforts to increase detection and treatment services for alcohol use problems, routine screening and brief interventions for internalized stigma must be incorporated within the normal clinical routine of primary health care.