The clinical importance of the isolation of nontuberculous mycobacteria (NTM) from respiratory specimens of stem cell transplant (SCT) recipients is not clear. We investigated the characteristics and clinical impact of NTM isolation in this population. Medical records of adult patients who underwent SCT at the blood and marrow transplantation center at a University Hospital in South Korea between January 2004 and December 2013 were retrospectively reviewed. Twenty-five of 2,658 patients were enrolled, an incidence of 0.94%. The most common NTM species isolated were Mycobacterium avium complex (n = 15) and Mycobacterium abscessus (n = 5). Sixteen patients were co-infected with other pathogens, including Aspergillus species (10 cases). Nonspecific pneumonia and cavitary pneumonia were the most common radiologic patterns. Sixteen patients had underlying lung graft-versus-host disease, including bronchiolitis obliterans (10 cases) with moderate obstructive lung defects. Whereas two of 10 patients who were treated for NTM died as a result of NTM progression, one of 15 patients who were not treated died of the same cause. This study shows that the incidence of respiratory NTM detection in SCT recipients was low and its virulence was not higher than expected. As patients frequently had concomitant infections and underlying lung diseases that made radiologic evaluation more difficult, we suggest that it would be advantageous to perform repeated microbiologic studies when NTM infection is clinically suspected.