The inherited deficiencies of protein C, protein S, antithrombin III, factor V Leiden mutation, prothrombin gene polymorphism, and antiphospholipids were studied in 53 Budd-Chiari syndrome (BCS) and 33 portal vein thrombosis (PVT) cases and compared with 223 age- and sex-matched controls. Protein C deficiency was detected in 7 (13.2%), protein S in 3 (5.7%), and antithrombin III in 2 (3.8%) of the BCS cases. Factor V Leiden was the most common risk factor, i.e., 14 of 53 (26.4%) in BCS cases followed by protein C, as compared with PVT cases, i.e., 2 of 33 (6.06%) and controls, i.e., 5 of 223 (2.3%). In PVT cases, protein C deficiency was present in 3 (9.09%), protein S deficiency in 1 (3.03%), and factor V Leiden mutation in 2 (6.06%) of the cases. The prothrombin gene polymorphism was not found in either the controls or the patients. The antiphospholipids were seen in 11 (20.75%) of the BCS cases and 6 (18.18%) of the PVT cases. Other acquired risk factors like pregnancy, surgery, and oral contraceptives were present in 8 (15.09%) of BCS and 3 (9.09%) of PVT cases. Thus overall, 59% of the BCS and 30% of the PVT cases could be explained by at least one of the etiologic factors studied.