In Malawi, it has been the practice for several years to obtain sputum for smear microscopy of acid-fast bacilli (AFB) from all patients with extrapulmonary tuberculosis (EPTB). We audited this practice, and determined in patients aged 315 years (i) the proportion of EPTB patients who had sputum smears examined, (ii) the number of sputum smears examined per patient, and (iii) the proportion of patients with EPTB who had sputum samples smear positive for AFB. Forty-one hospitals (3 central, 22 district and 16 mission) performing smear microscopy and registering EPTB patients were visited in 1998 and 1999, and a retrospective and prospective study was carried out using TB registers and laboratory sputum registers. In the retrospective study, 1124 (69%) of the 1637 patients with EPTB had sputum smears examined; 988 (88%) of the 1124 submitted 3 sputum specimens. In the prospective study, 2026 (84%) of the 2411 patients with EPTB had sputum smears examined: 94% of the 2026 submitted 3 sputum specimens. In both studies, high rates of sputum submission were found in patients with pleural effusion, miliary TB, lymphadenopathy and pericardial effusion. In the prospective study, only 34 (1.7%) EPTB patients submitting sputum were smear positive, and the proportion who were smear positive exceeded 3% only in patients with lymphadenopathy, miliary TB and TB meningitis. As a result of this study, the Malawi TB Control Programme has changed its policy, and now only insists on sputum-smear examination if patients with EPTB have a cough for >3 weeks. These policy changes will be audited by further operational research.