ObjectiveTo evaluate the proposed WHO/UNAIDS criteria for initiating co-trimoxazole prophylaxis in adult HIV-infected patients in Africa [WHO clinical stages 2–4 or CD4 count < 500 × 106/l or total lymphocyte count (TLC) equivalent].DesignObservational cohort study of 5-year follow-up.SettingAdult HIV clinics, University of Cape Town, South Africa.MethodsEffect of prophylactic low dose co-trimoxazole (480 mg per day or 960 mg three times per week) on survival and morbidity was assessed in patients stratified by WHO clinical stage, CD4 T-lymphocyte count or TLC. Patients receiving antiretroviral therapy were excluded.ResultsCo-trimoxazole reduced mortality [adjusted hazard ratio (AHR), 0.56; 95% confidence interval (CI), 0.33–0.85;P> 0.001] and the incidence of severe HIV-related illnesses (AHR, 0.52; 95% CI, 0.38–0.68;P< 0.001) in patients with evidence of advanced immune suppression on clinical (WHO stages 3 and 4) or laboratory assessment (TLC < 1250 × 106/l or CD4 count < 200 × 106/l). No significant evidence of efficacy was found in patients with WHO stage 2 or CD4 count 200–500 × 106/l/TLC 1250–2000 × 106/l. If we had applied the WHO/UNAIDS recommendations 88.3% of our patients would have received co-trimoxazole prophylaxis at their initial clinic visit.ConclusionCo-trimoxazole in HIV-infected adults from an area in whichPneumocystis cariniipneumonia is uncommon demonstrated a survival benefit consistent with previous randomized trials. Further studies are needed to assess the optimal time of commencement of prophylaxis, as widespread co-trimoxazole use will lead to increasing antimicrobial resistance to other major pathogens in Africa.