SETTING: Isoniazid therapy was shown to be 70% effective at preventing tuberculosis in HIV-infected, PPD-positive Ugandan adults, but the feasibility of implementation outside an efficacy trial has not been established. OBJECTIVE: To study uptake, adherence and feasibility of a 6-month course of isoniazid preventive therapy in community-based HIV clinics in Uganda. DESIGN: Observational cohort study describing selection of patients and adherence to isoniazid 300 mg daily. Adherence was measured by clinic attendance, pill counts and urine isoniazid metabolite testing. Implementation was costed on a service delivery basis. RESULTS: Of 1597 cohort members, 22% were PPD-positive. Over 18 months, 193 PPD-positive individuals were assessed for prophylaxis and 98 (51%) were enrolled. Of those enrolled, 74 (76%) completed their course of isoniazid therapy, and 80% were fully adherent. Symptoms or previous treatment for tuberculosis and suspicion of tuberculous lymphadenopathy were the main reasons for exclusion. The additional cost of providing this service was US $14,549. CONCLUSION: Clinics specialising in the care of persons with HIV/AIDS can successfully implement isoniazid prophylaxis. Difficulties in excluding active tuberculosis and the costs of running the programme may limit its widespread implementation.