Very few data are available on the comparison of infectious complications in peripheral blood stem cell transplantation (PBSCT) and bone marrow transplant (BMT). The objective of this study was to evaluate the severity and frequency of infectious complications in patients randomized to receive PBSCT or BMT. We retrospectively reviewed the charts of all patients included in a randomized clinical trial comparing PBSCT (27 patients) and BMT (29 patients). We analyzed two periods: pre‐engraftment and post‐engraftment. In the pre‐engraftment period, we compared the two groups with respect to the duration of neutropenia, antibiotic use and hospitalization, and documentation of infection. In the post‐engraftment period, we analyzed the occurrence and severity of graft‐versus‐host disease (GVHD), duration of cyclosporine, corticosteroids, antibiotic, antiviral and antifungal prophylaxis, number of episodes of infection, and death rates. Patients receiving PBSCT had shorter duration of neutropenia, but there were no differences in the incidence of infections or duration of antibiotic therapy. Patients receiving PBSCT had a higher incidence of extensive chronic GVHD (65% vs. 39%, P=0.08), longer duration of cyclosporine use (risk ratio [RR] 1.97), corticosteroids (RR 1.66), antibacterial (RR 2.60), antifungal (RR 2.50), anti‐Pneumocystis carinii (RR 2.06) and anti‐cytomegalovirus (RR 1.44) prophylaxis, and more infectious episodes (3.65 vs. 2.32 per 1000 days at risk, RR 1.57). There were no differences in death rates. Multivariate analysis identified the use of steroids as the most significant variable associated with infectious episodes. PBSCT was associated with more infections in the post‐engraftment period.