Infectious complications remain an important cause of death in hematopoietic stem cell transplant (HSCT) recipients. We undertook a 20-year (1988-2007) retrospective review of all autopsies performed on HSCT recipients in our institution, with emphasis on infections, especially fungal infections, as the cause of death. Of the 2,943 autopsies performed in our institution from 1988 to 2007, 395 (13.4%) involved HSCT recipients (117 pediatric; 278 adult). Of the patients, 298 had received allogeneic, 46 autologous, 41 umbilical cord blood, and 3 autologous plus allogeneic types, and 7 were unknown HSCT types. The most common causes of death were pulmonary complications, occurring in 247 (62.5%) of 395 cases. In 178 cases (45.1%), microorganisms (viral, bacterial, and/or fungal) were documented at autopsy in one or more organs and contributed to the cause of death. Fungal infections were found in 23.5% of cases, but their frequency as a cause of death decreased throughout this study, from 30.3% in the 1988-1992 period to 10.9% in the 2003-2007 period.