Objective To evaluate the performance of an algorithm based on WHO recommendations for diagnosis of smear-negative pulmonary tuberculosis in HIV-negative patients. Methods We recruited HIV-negative patients with clinical suspicion of tuberculosis who had had three negative sputum smears in Lima, Peru. All included subjects underwent a complete anamnesis, physical examination and chest X-ray, and had a sputum specimen cultured in Ogawa, Middlebrook 7H9 media and MGIT®. We applied an algorithm based on WHO recommendations to classify patients as having tuberculosis or not. The diagnostic performance of the algorithm was evaluated comparing its results against the reference standard of a positive culture for M. tuberculosis in either of the media used. Results A total of 264 of the 285 patients included (92.6%) completed evaluation and follow up. Of these, 70 (26.5%) had a positive culture for M. tuberculosis. Clinical response to a broad spectrum course of antibiotics was good in 32 of these 70 patients (45.7; 95%CI 34.0-57.4%). Overall, the algorithm attained a sensitivity of 22.9% (95% CI 13.1-32.7%) and a specificity of 95.4 % (95% CI 92.4-98.3%) compared to culture results. The positive likelihood ratio was 4.93 and the negative likelihood ratio was 0.81. Conclusions The sensitivity and negative likelihood ratio of the algorithm is poor. It should be re-evaluated, and possibly adapted to local circumstances before further use. The clinical response to an antibiotic trial is the most important component to reassess. We also suggest considering performing chest X-ray earlier in the diagnostic work-up. © 2011 Blackwell Publishing Ltd.