The haematological indications for allogeneic stem cell transplantation can be broadly divided into non-malignant and malignant disorders. We compared the incidence and risk factors for post-transplant cytomegalovirus (CMV) infections between these two biologically diverse subgroups of haematological conditions. Out of 105 allogeneic transplants, 64 and 41 were for underlying non-malignant and malignant indications respectively. CMV infections were significantly more frequent (P=0.016) in the malignant subgroup. Pre-transplant recipient CMV seropositivity in both subgroups (negative versus positive; non-malignant,P=0.023; malignant, p<0.001), donor seropositivity (P=0.002) and acute graft-versus-host disease (GVHD) (P=0.02) in the non-malignant subgroup and > or =3 courses of previous cytotoxic therapy (P=0.023) in the malignant subgroup were found to be associated with an increased risk of CMV infections. On multivariate analysis, donor seropositivity in the non-malignant patients (negative versus positive,P=0.022; odds ratio: 0.18) and recipient seropositivity in patients with malignancies (negative versus positive; P=0.001, odds ratio: 0.01) were identified to be significant factors for risk of CMV infection.