To improve the safety and effectiveness of warfarin (WF) therapy, the initial dose trends to be practically decided based on single nucleotide polymorphism (SNP) genotyping of two genes, cytochrome P450 (CYP) 2C9 and vitamin K epoxide reductase complex1 (VKORC1). We encountered a 43-year-old female who was hospitalized for investigation and treatment because of intermittent convulsive seizures. Right brain cortical vein thrombi were confirmed by magnetic resonance imaging (MRI) scan; therefore, a 3 mg dose of WF was empirically initiated. The prothrombin time (PT), expressed as the international normalized ratio (INR), did not change at all, even when WF was increased to a dose of 11 mg/day. Direct sequence analysis revealed *3 in CYP2C9 and 3673 GA, 6484 CT, 6853 GC and 9041 GA in VKORC1, indicating that the genotypic pattern of the two genes is the responsible SNP for the moderate phenotype on WF sensitivity. Conclusively, our case may present an unknown mechanism other than the concern mentioned above.