Background: Thrombosis is an increasingly recognized complication of childhood malignancy and its treatment. The etiology of pediatric cancer-related thrombosis is multifactorial and not well understood at present. The aim of this study was to evaluate the prevalence of common prothrombotic genetic conditions in children with cancer, the frequency of thrombosis, and the role of inherited thrombophilia in the development of thrombosis in a pediatric oncology population. Methods: Forty-seven children (36 treated for hematological malignancies and 11 for solid tumors) with the median age of 8.8. years (range 0.4 – 19.3 years) were included in the study. Genetic polymorphisms of Factor V Leiden, prothrombin G20210A mutation, and methylenetetrahydrofolate reductase (MTHFR) C677T were determined by real-time polymerase chain reaction-based DNA analysis. Results: Four (8.5%) patients were heterozygous for Factor V Leiden, 3 (6.4%) were heterozygous for prothrombin G20210A mutation, and 3 (6.4%) were homozygous for MTHFR C677T mutation. All patients had inserted central venous lines. Four (8.5%) children had documented thrombosis, 3 of which were located in the upper venous system. Two of four patients with thrombosis had Factor V Leiden heterozygosity. Conclusions: Thrombosis is an important complication of childhood cancer. Our results suggest that congenital prothrombotic abnormalities could be implicated in increasing the risk of thrombosis and support a recommendation that children with cancer be evaluated for inherited thrombophilia.