We performed a retrospective cohort study to find out whether the use of reduced-intensity conditioning (RIC) might reduce the risk of early death from pneumonia. Pneumonia-associated deaths were evaluated in 691 hematopoietic stem cell transplantation (HSCT) patients. The majority had a hematological malignancy (n = 504) and an HLA-matched donor (n = 584). RIC was given to 336 patients and myeloablative conditioning (MAC) to 355. Data concerning radiology, culture and autopsy results were evaluated together with risk factors for death related to pneumonia within or after 100 d after HSCT (early and overall pneumonia). In 60 patients, pneumonia contributed to death (early n = 17). The cumulative incidence of early pneumonia-related death was 2.8% and 2.1% in MAC and RIC patients, respectively. The cumulative incidence of overall pneumonia-related death was 8.2% and 10.5%, respectively. In 40 patients, (67%) an etiology could be established, with 19 patients having proven or probable mold infection. In the multivariate analyses, acute graft-versus-host disease (GVHD) grades II–IV, cytomegalovirus (CMV) infection and having received mesenchymal stromal cells (MSCs) were factors associated with overall pneumonia-related death. Bacteremia and a previous HSCT were associated with early pneumonia-related death. RIC did not reduce the incidence of early death associated with pneumonia. Acute GVHD II–IV, CMV infection and MSC treatment were factors associated with pneumonia-related death. Mold infection was the most common contributor to pneumonia-related death in HSCT patients.