Between 1995 and 2002, nine cases of nontuberculous mycobacterium (NTM) were isolated from 462 allogeneic stem cell transplant (SCT) recipients (1.9%), and none from 139 autologous cases. They included three cases each of Mycobacterium fortuitum and M. chelonae, and single cases of M. scrofalaceum, M. gordonnae and M. avium complex. Seven cases were respiratory, including five cases requiring treatment, and two involved infected catheters and vascular conduits. Compared with nine cases of mycobacterium tuberculosis (MTB) isolated in the same period, NTM isolation occurred later after HSCT and involved more unrelated donors. Important risk factors for NTM infection included significant aGVHD (P=0.043), leukemia relapse (P=0.022), MUD and mismatch SCT (P<0.001) and existence of BO (P<0.001). Coinfection with aspergillus was common. Invasive NTM disease required prolonged antimicrobial treatment in five cases due to M. fortuitum and M. chelonae. With better MTB prophylaxis, intensive immunosuppression and better awareness, NTM has become an emerging threat in oriental allogeneic HSCT recipients. The cutoff between colonization and infection, and the threshold for starting treatment is unclear. NTM isolation is a marker for severe immunosuppression and poor prognosis. When there is doubt over species identity or extent of infection, broad-spectrum cover may be prudent.