Presumptive pulmonary tuberculosis (PTB) patients whose sputum are detected to be smear negative for acid fast bacilli (AFB) present a significant challenge for a treating physician. Initiating these patients on anti tuberculous treatment (ATT) on empirical basis is not a good strategy as many were found to be sputum culture for tuberculosis negative on further evaluation according to many previous studies. In India due to resource limited settings and lack of knowledge about newest diagnostic modalities patients are often initiated only on the basis of characteristic clinical symptoms and chest radiographic abnormalities. This study was conducted to identify the advantage of application of sputum cartridge based nucleic acid amplification test (CBNAAT) in sputum AFB smear negative presumptive pulmonary TB patients. Our study concluded that clinical symptoms and radiological characteristics cannot differentiate TB patients from non-TB patients. Treating patients only on empirical basis would have resulted in unnecessary treatment of 41 patients.