We report a retrospective analysis of Cytomegalovirus (CMV) infection: incidence, recurrence, resistance, and subsequent disease of 81 children who underwent allogenic hematopoietic stem cell transplantation (HSCT). The recipient and/or donor's CMV serology was positive prior to transplant [recipient (R+) and/or donor (D+)]. CMV was monitored by RT-PCR starting from the first week post transplant. Forty patients showed CMV infection (49, 5%). Of them 10 manifested CMV disease leading to four deaths. In univariate analysis, factors associated with CMV infection were CMV R+ P < .01, CMV R+/D+ pair P < .01, nonbone marrow (BM) stem cell source P < .05, nonirradiation conditioning regimen P < .05, Antithymocyte globulin (ATG) P < .01. Factors associated with CMV resistance were: >1 HLA allele mismatch P < .05, CMV R +/D-pair P < .01, CMV D-P < .01, non-BM P < .05, nongenoidentical transplant P < .01. CMV disease was influenced by >1 HLA allele mismatch (P < .001), non-BM (P < .01). On multivariate analysis, CMV R+/D- (P < .05), corticosteroids ≥2 mg/kg P < .01, ATG P < .01 and non-BM (P < .05) were independent factors for CMV infection. CMV R+ transplant is associated with more CMV infection and resistance to preemptive treatment. Prolonged immune suppression (IS) worsens outcome of CMV infection and should be shortened whenever possible.