Deep venous thrombosis (DVT) in children is more often associated with underlying pathological conditions than with hereditary thrombophilia. The present study is a retrospective analysis of thrombophilia in 285 pediatric patients with venous thrombosis at different sites. Four common thrombophilia markers, that is protein C, protein S, antithrombin III, and factor V Leiden (FVL) mutation, were analyzed. Thrombosis in hepatic and portal veins was more common in pediatric patients (73%) when compared to other sites (27%). Overall, hereditary thrombophilia accounted for 15.5% of the patients with venous thrombosis. The FVL mutation, which was the major causative factor in Budd-Chiari syndrome and portal vein thrombosis cases in the adult group, was not a major contributing factor in pediatric group, that is, 1.8% of the patients. In conclusion, the risk factors for venous thrombosis vary in different age groups.