We describe a 16-year-old girl with malignant fibrous histiocytoma (MFH) of the heart complicated by factor XI deficiency. The preoperative diagnosis was left atrial myxoma. We decided to perform the operation owing to a normal bleeding time. Operative findings suggested a malignant tumor. The patient was a Jehovah's Witness, and extensive excision was not performed because blood transfusion was not allowed. We resected as much of the tumor and left atrial appendage as possible. The pathologic diagnosis was MFH. Excessive bleeding was not observed during the operation. Bleeding time helps to determine whether a surgical procedure is indicated in patients with factor XI deficiency.