Chemotherapy and/or radiotherapy used as conditioning regimens before autologous or allogeneic haematopoietic cell transplantations (HCTs) cause neutropenia, which is the main reason for bloodstream infections. Autologous HCTs are considered to be superior to allogeneic HCTs in terms of infection outcome. A previous analysis suggested that patients with allogeneic HCTs are exposed to a reduced infection hazard and that an unfavourable infection outcome of allogeneic HCTs may be mediated through prolonged neutropenia. Therefore, we investigated whether allogeneic HCTs initially lead to fewer infections. We evaluated data from a prospective non-randomized multi-centre cohort study, with a total of 1616 patients. Of these, 703 patients received autologous and 913 patients received allogeneic HCTs from January 2000 to June 2004. The retrospective analysis used simultaneous confidence bands for the cumulative infection probability in the presence of competing risks. Patients with allogeneic HCTs experienced fewer infections during the early phase of neutropenia. As patients with autologous HCTs are not necessarily subject to antibiotic prophylaxis, a future study should investigate this policy. A limitation of the analysis is that it did not find the effect of crossing cumulative infection probabilities to be significant.