There is little information on a country-wide basis in sub-Saharan Africa about how the diagnosis of extra-pulmonary tuberculosis (EPTB) is made. A country-wide cross-sectional study was carried out in 40 non-private hospitals in Malawi which register and treat (TB) patients in order to assess diagnostic practices in adults registered with EPTB. All patients aged 15 years and above in hospital on treatment for EPTB were reviewed usingTB registers, case note files and clinical assessment. There were 244 patients, 132 men and 112 women whose mean age was 36 years. In 138 (57%) patients, all appropriate procedures and investigations, commensurate with hospital resources, had been carried out. Of 171 EPTB patients with cough for 3 weeks or longer, 138 (81%) submitted sputum specimens for smear microscopy of acid-fast bacilli (AFB). A confirmed diagnosis ofTB was made in 15 (6%) patients based on finding AFB or caseating granulomas in specimens. In 157 (64%) patients, the diagnosis of EPTB was considered to be correct. In 46 (19%) patients the diagnosis was considered to be TB, although different from the type of EPTB with which the patient was registered. In 39 (16%) patients an alternative non-TB diagnosis was made and in two (1%) patients it was not possible to make a decision. Diagnostic practices need to be improved, and ways of doing this are discussed.