Non-myeloablative (NMA) allogeneic donor SCT for patients with relapsed lymphoma is associated with lower treatment-related mortality (TRM). However, the impact of conditioning intensity on post transplant infections remains unclear. We evaluated infections in 141 consecutive patients with lymphoma who were allografted using NMA (n = 76) or myeloablative (MA; n = 65) conditioning regimens. Using infection incidence density per 1000 patient days, we accounted for all infectious episodes during the first post transplant year. Before neutrophil engraftment, the NMA cohort had a 53% lower rate of bacterial infection (relative risk = 0.47; P = 0.06), whereas after engraftment the density of bacterial infections was similar in the two groups. In the first month, both invasive fungal infections and viral infections were twofold less frequent (P = 0.22; P = 0.06) in NMA patients. Late viral and fungal infections as well as CMV reactivation were infrequent after either conditioning intensity. The 1-year infection-related mortality was significantly lower after NMA conditioning (NMA 9% (3-16%) vs MA 22% (11 - 40%); P = 0.03). NMA allogeneic transplantation for lymphoma patients results in substantially fewer early infections and lower infection-related deaths, although the similar frequency of later infections suggests that immune reconstitution is delayed with either conditioning intensity.