We enrolled 52 patients with suspected pulmonary nontuberculous mycobacterial (NTM) infections with a follow-up period of at least two years, in which NTM organisms had not been detected by bronchofiberscopy. Symptoms, radiographic findings, and results of the microbiologic re-examination were retrospectively reviewed. During a median follow-up period of 68 months (range, 24–124 months), the symptoms deteriorated in six cases, and the radiographic findings deteriorated in 12 cases. In none of the 14 cases were NTM organisms detected on re-examination by bronchoscopy. In two cases, the organisms were detected in sputum samples. On the basis of the negative results of re-examination by bronchofiberscopy in this study, conditions other than NTM infections should be considered when symptoms and radiologic findings deteriorate and there is a negative sputum examination for NTM.