To assess whether there is any difference in postoperative morbidity and mortality after pneumonectomy between patients with multidrug-resistant tuberculosis (MDR-TB) and patients with non-tuberculous mycobacterial (NTM) infections. Between January 2000 and December 2007, 61 patients with MDR-TB and 60 patients with NTM infections underwent 66 and 64 pulmonary resections, respectively. Of these, 33 patients were analyzed who underwent a pneumonectomy, including 22 patients with MDR-TB (seven right, 15 left) and 11 patients with NTM infections (seven right, four left). All bronchial stumps were covered with the latissimus dorsi. Patients with NTM infections were predominantly more female, older, thinner, and presented with a higher frequency of culture-positive sputum at operation than patients with MDR-TB. Operative mortality was zero. Morbidities were bronchial stump dehiscence (n=1) and mycobacterial empyema (n=1) for patients with MDR-TB, and acute respiratory failure (n=1), bronchial stump dehiscence (n=5) and mycobacterial empyema (n=2) for patients with NTM infections. Prevalence of bronchial stump dehiscence was significantly higher in patients with NTM infections (P=0.010). Five of six dehiscences occurred after right pneumonectomy. The optimal management of the bronchial stump in the setting of pneumonectomy for NTM infections needs further investigation.