The aim of the present study was to investigate whether real-time polymerase chain reaction (PCR) has a low identification rate for samples with low acid-fast bacilli (AFB) grades, including those obtained using bronchoscopy. When 50 smear-positive samples were compared by AFB score and PCR result, PCR was 100% successful in identifying AFB 2+ and AFB 3+ samples. However, only 14 of 26 (52%) AFB 1+ samples were identified. In paucibacillary smear-positive samples, PCR is not reliable enough to exclude tuberculosis, but in smear-positive patients with high AFB grades PCR can immediately change the clinical management of the disease.