Cytomegalovirus (CMV) is one of the major causes of morbidity and mortality after hematopoetic stem cell transplantations (HSCT). The purpose of the study was to analyze risk factors of CMV disease in children undergoing HSCT. A total of 110 children who undergone hematopoetic stem cells transplantation were analyzed. In 16 patients (14.5%) CMV antigenemia in white blood cells was diagnosed. Most patients with CMV infection had undergone alloHSCT; one patient had undergone autologous transplantation. Second CMV reactivation in 4 of 16 patients was observed. Acute GvHD occurred in 11/15 patients. Early onset of CMV infection in 13/16 patients and late onset in 3/16 patients were diagnosed. CMV serological status of the donor and recipient before transplantation in children with CMV antigenemia was analyzed. The risk factors of CMV infection in analyzed group of children were type of transplant, recipient seropositivity before transplantation, and presence and intensity of GvHD. In most cases reactivation of CMV infection was diagnosed. CMV infection can also occur in the late post-transplantation period. CMV reactivation can occur in patients after autologous HSCT.