The risk and outcome of infection in febrile neutropenic patients is mainly determined by the duration of neutropenia, the underlying disease or the treatment. This study was undertaken to compare infections and the outcome after conventional chemotherapy (CCT), allogeneic PBSC transplantation (alloPBSCT) or autologous PBSC transplantation (autoPBSCT), during the period of neutropenia, in a single center. A total of 145 patients (50 in CCT group, 50 in alloPBSCT and 45 in autoPBSCT) were evaluated. In the alloPBSCT group, 86% of the patients (43/50), in the autoPBSCT group 93% of the patients (42/45) and in the CCT group 92% (46/50) of the patients had at least one febrile episode during their neutropenic period (P > 0.05). Microbiologically and/or clinically documented infection rates were 50% (25/50), 42% (19/45) and 48% (24/50) respectively. Gram-positive pathogens, mostly coagulase-negative staphylococci were the most frequent cause of bacteremias in all groups. The frequency of CNS infections was significantly higher in the alloPBSCT and autoPBSCT groups compared to the CCT group (P < 0. 008 and P < 0.04, respectively). Catheter infections were frequent in the PBSCT groups and pulmonary infections were more frequent in the CCT group (P < 0.05). The CCT group needed longer antibiotic usage compared to the alloPBSCT group (P < 0.006). The duration of neutropenia and the type of treatment given, does not affect the rate of febrile episodes, but affects the type of infections in febrile neutropenic patients.