Coagulation factor V (FV) is both procoagulant and anticoagulant functions. Congenital FV abnormality, which are caused by mutations in the FV gene, are characterized by a tendency to bleed. However, FV-R506Q (FV) is the most common FV abnormality that eliminates an activated protein C (APC) cleavage site, resulting in the occurrence of deep venous thrombosis (DVT). In Japan, the thrombotic predisposition caused by FV and FV molecular abnormalities was believed to be nonexistent. We did, however, report the first case in Japan of a young patient with FV abnormality-related thrombosis. The recurrent DVT in this case was caused by a novel mutation of FV-W1920R (FV), located in the C1 domain and far from the APC cleavage sites. We considered the possibility that there were cases of FV-related thrombotic predisposition that had gone undetected in Japan. We thoroughly examined FV-related anticoagulant function to understand the pathogenesis of thrombosis caused by FV abnormality. Furthermore, using recombinant thrombomodulin, we successfully developed a novel assay with clot waveform analysis for the rapid detection of FV deficiency with APC resistance. Other FV abnormality-related thrombosis has been reported in Japan in recent years, and we hope to further clarify the FV-related thrombotic predisposition in the future.