Two pediatric patients with Budd-Chiari syndrome are reported, who were heterozygous for factor V Leiden mutation. The first patient was falsely diagnosed with type II protein C deficiency, and the second was initially found to have decreased protein C activity based on a protein C clotting assay. Retesting by protein C chromogenic assay indicated that protein C activity was normal in both children. In patients with Budd-Chiari syndrome, low levels of protein C antigen and activity should be interpreted with caution, and within the context of factor V Leiden mutation status, parents' results, severity of liver dysfunction, and the type of protein C assay performed in order to avoid misdiagnosing protein C deficiency.