Infections due to post transplant immune deficiency is a major problem following allogeneic stem cell transplantation, particularly in patients receiving cord blood or T-cell depleted haploidentical transplants. We evaluated the incidence and type of infectious complications that occurred in these two types of transplant for 65 patients, 37 cord blood and 28 haploidentical, who received the same conditioning regimen: fludarabine, melphalan and thiotepa. While incidence of infections appeared similar in both types of transplant, viral infections were more frequent than bacterial or fungal infections and were the most common cause of death in both groups. Patients in the haploidentical group were 1.7 times (95% CI: 1.1 to 2.5) more likely to have a viral infection (p=0.013). Bacterial, fungal and CMV infections still quite frequent but contributed less to mortality. Pneumonia was the most common clinical syndrome and the number one cause of death in both groups. Both pneumonia and bacteremia occurred within the first 100 days in the majority of HSCT patients while CBT patients had a bimodal distribution, with more than one third of episodes after 6 months post transplant.