<h2>SETTING:</h2>A tertiary referral hospital in Bangkok, Thailand.<h2>OBJECTIVES:</h2>To evaluate the efficacy of a bronchoalveolar lavage fluid (BALF) tuberculosis (TB) polymerase chain reaction (PCR) assay for the diagnosis of sputum smear-negative pulmonary TB (PTB) and the usefulness of a drug-resistant (DR) TB-PCR assay compared with standard drug susceptibility testing (DST).<h2>DESIGN:</h2>BALF samples from 918 patients with acid-fast bacilli (AFB) negative sputum smears who underwent bronchoscopy for diagnostic evaluations of pulmonary diseases were prospectively determined for specific genetic elements of TB using the Anyplex(TM) MTB/NTM Real-Time Detection kit. Positive TB-PCR samples were subsequently evaluated for DR-TB using the Anyplex II MTB/MDR Detection kit.<h2>RESULTS:</h2>A total of 224 patients were finally diagnosed with PTB. The sensitivity, specificity, positive predictive value and negative predictive value of the TB-PCR assay were respectively 38.8%, 100%, 100%, and 83.5%. The TB-PCR assay was more sensitive than culture (30.4%) and smear (6.7%). Of the 68 TB-positive culture samples, three cases with either isoniazid (INH) or rifampicin (RMP) resistance were detected by DST. The Anyplex II MTB/MDR assay provided similar results.<h2>CONCLUSIONS:</h2>The BALF TB-PCR assay is a useful tool in the diagnosis of sputum smear-negative PTB. It can also provide INH and RMP susceptibility patterns similar to those of standard DST.