Objective: To establish the aetiology of chronic cough in HIV-infected patients with negative sputum smears for Acid Fast Bacilli (AFB). Design: A cross-sectional descriptive study. Setting: Kenyatta National Hospital, a tertiary referral centre in Kenya Subjects: Sixty five HIV-infected adults presenting with chronic cough and negative sputum smears for AFBs. Results: Sixty-two patients were included in the final analysis. Aetiology of chronic cough was established in 42 (68%) patients. Pneumocystis jiroveci, bacterial pneumonia and Mycobacterium tuberculosis were diagnosed in 22 (35.5%), 17 (27.4%) and 14 (22.5%) patients respectively. Majority (98%) of patients with a diagnosis had multiple causes established in them. Ciprofloxacin had activity against 91% of the isolated organisms while Penicillin was active against 35% only. Conclusion: This study documents Pneumocystis jiroveci pneumonia as a common cause of morbidity in a subset of HIV infected patients with chronic cough and negative sputum smears for AFB in Kenya.