Background: Infections constitute a major problem for patients during oncological treatment or undergoing hematopoietic stem cell transplantation (HCT). Objective: The aim of the study was to analyze the epidemiology of viral infections in children during anticancer therapy (PHO, pediatric haematology and oncology) or after HCT over a period of consecutive 6 years in a single-centre study. Patients and methods: During this period, a total number of 182 HCTs were performed, and 306 children were newly diagnosed for malignancy. Incidence, hazard risk and outcome of infections were analyzed. Results: The cumulative incidence of viral infections was 61.7% in allo-HCT, 8.5% in PHO, and 4.1% in auto-HCT patients. The overall risk of viral infection in HCT patients was 17.3-fold higher (p < 0.0001) than in PHO patients. The risk was 30-fold higher for CMV and 63-fold higher for EBV, while the risk was comparable for influenza and adenovirus infection. Infections with polyoma BKV occurred only in HCT patients after allo-HCT. Factors contributing to increased risk of viral infections in allo-HCT patients both in uni-and multivariate analysis were: male sex, diagnosis of acute leukemia, alternative donor, CMV positive serostatus in recipient and/or donor, acute and chronic GVHD. All patients except two allo-HCT children survived viral infections. The cause of death were influenza and EBV-PTLD. Conclusions: The risk of viral infections in allo-HCT patients is much higher than in auto-HSCT and PHO patients, while the outcome of infections was better in the PHO and auto-HCT setting.