We aimed to characterize the infectious complications of autologous bone marrow (AuBMT) and peripheral stem cell transplantation (PSCT) in patients with refractory leukemia and lymphoma. We performed a retrospective analysis of all patients (n = 56) with refractory leukemia or lymphoma treated with AuBMT or PSCT at Memorial Sloan-Kettering Cancer Center from January 1993 to July 1994. Records were available in 55, of whom 33 (60%) received AuBMT and 22 (40%) PSCT. Fifteen (27%) developed complicated infections, including 13 (39%) treated with AuBMT and two (9%) with PSCT. Complicated infections were caused by bacterial (11 episodes), fungal (four episodes), and viral (four episodes) pathogens. Five (9%) infections were fatal. In a multivariate model, only duration of neutropenia was significantly associated with development of complicated infection (P = 0.006). Thus, 27% of patients with refractory leukemia or lymphoma treated with AuBMT or PSCT developed complicated infections and 9% died of infection. Prolonged neutropenia was significantly associated with development of infection. Patients receiving PSCT had significantly lower rates of complicated infection, presumably due to the associated shorter duration of neutropenia. Future studies are needed to define the role of PSCT as treatment for refractory neoplastic disease.