BACKGROUND: In sub-Saharan African countries, the high proportion of smear-negative pulmonary TB (SNTB) and extrapulmonary TB (EPTB) contributes to a delay in TB diagnosis and treatment. We evaluated the TB diagnostic process of adult patients with presumptive TB in a referral hospital in Mozambique according to the 2007 WHO recommendations for the diagnosis and treatment of SNTB and EPTB in HIV-prevalent resource-poor settings. METHODS: This was a retrospective, cross-sectional study using medical records of patients admitted in June-July 2009. RESULTS: Overall, 514 patient records were screened, providing 234 presumptive TB patients. There were 70 deaths (29.9%). The evaluation of danger signs was never complete. HIV status was known for 175/234 patients (74.8%), 140 (80.0%) of whom were HIV-positive. A sputum smear microscopy (SSM) result was obtained for 59/234 patients (25.2%). SSM results were positive in 8/59 patients (13.6%). Chest radiography was done in 150/234 patients (64.1%) and 103 (68.7%) were abnormal. A total of 66 patients (28.2%) received TB treatment. CONCLUSIONS: The TB diagnostic process in this Mozambican hospital remained largely incomplete according to WHO recommendations and few patients with presumptive TB were identified as TB patients. Deficiencies as described should prompt reconsideration of WHO guideline content and feasibility.