Cytomegalovirus (CMV) infection remains an important cause of morbidity and mortality following allogeneic stem cell transplantation (SCT). We wanted to study if the high sero-prevalence seen in our population translated into a high incidence of CMV infection following SCT. This is a retrospective analysis of patients who underwent allogeneic SCT between January 2008 and December 2012 at our centre. 475 patients underwent allogeneic SCT for malignant (46.5%) and non-malignant (53.5%) haematological disorders. 463 (97.4%) SCT recipients and 403 (84.8%) SCT donors were IgG seropositive for CMV. CMV reactivation within 100 days post SCT was seen in 174 (36.6%) at a median of 41 days (range 10-100) post SCT. Ganciclovir was used in 166 patients (95.4%) for a mean duration of 16 days (range 5-32). 157 patients (90%) responded to therapy. Sixty-six patients (42.3%) had secondary reactivation of the virus. Use of a male donor (p = 0.000), donor and recipient age [ 15 (p = 0.005 and 0.000), unrelated donor (p = 0.000), degree of HLA mismatch (p = 0.000), occurrence of acute GVHD (p = 0.000) and steroid refractory acute GVHD (p = 0.026) were identified as risk factors for CMV reactivation while early neutrophil recovery (\ 15 days) was found to be protective (p = 0.004). On multivariate analysis, male donor (p = 0.042), degree of HLA mismatch (p = 0.006), the occurrence of acute GVHD (p = 0.000) and steroid refractory acute GVHD (p = 0.031) continued to remain significant. 5-year overall survival was significantly better in patients without CMV reactivation compared to those who developed reactivation of CMV (68.9 ± 3.7 vs 58.2 ± 4.9% p = 0.004). The incidence of CMV infection does not seem to be higher despite a high sero-prevalence of CMV. However, patients who developed CMV infection post SCT had inferior outcomes.