Infectious complications remain a major problem contributing to significant mortality after hematopoietic allogeneic stem cell transplantation (HSCT). Few studies have previously analyzed mortality due to late infections. Forty-four patients dying from an infectious complication were identified from a cohort of 688 consecutive patients surviving more than 6 months without relapse. A control group of 162 patients was selected using the year of HSCT as the matching criterion. Out of 44 patients, 30 (68%) died from pneumonia, 7/44 (16%) from sepsis, 5/44 (11%) from central nervous system infection and 2/44 (4.5%) from disseminated varicella. The cumulative incidences of different types of infection were 1.6% for viral, 1.5% for bacterial and 1.3% for fungal infections and 0.15% for Pneumocystis jirovecii pneumonia. The majority (66%) of the lethal infections occurred within 18 months after HSCT. Acute GVHD (relative risk (RR): 7.19, P<0.0001), chronic GVHD (RR: 6.49, P<0.001), CMV infection (RR: 4.69, P=0.001), mismatched or unrelated donor (RR: 3.86, P=0.004) and TBI (RR: 2.65, P=0.047) were independent risk factors of dying from a late infection. In conclusion, infections occurring later than 6 months after HSCT are important contributors to late non-relapse mortality after HSCT. CMV infection or acute GVHD markedly increase the risk.