We report a case of intolerance to warfarin. A 20-year-old woman with toe pain was diagnosed with myxoma with multiple systemic embolisms. She was prescribed warfarin for remaining embolic pain after myxoma excision and mitral annuloplasty. Even on 1 mg of warfarin, the international normalized ratio was much increased. The patient was found to have cytochrome P450 2C9 (CYP2C9)*3/*3 and vitamin K epoxide reductase complex subunit 1 (VKORC1) 1639AA genotype, which is extremely rare in Koreans. Based on this result, we assessed the potential risks and benefits of warfarin and decided to switch to aspirin because the risk of bleeding was considered to be too high.