A 50-year-old male patient with hypertrophic cardiomyopathy and atrial fibrillation was anticoagulated, with warfarin following insertion of a cardioverter defibrillator. He became markedly over anticoagulated after standard moderate induction doses of warfarin. His baseline prothrombin time was prolonged and further investigation showed the patient to have a mild factor VII deficiency. He was restarted on low-dose warfarin and successfully stabilized with a target international normalized ratio (INR) of 3.0 (range 2.5-3.5). We used the data from factor VII levels and thrombin generation studies before and after anticoagulation to control dosage and to decide on a suitable therapeutic range for the INR. Molecular studies showed him to have two separate mutations in the factor VII gene. This report highlights the importance of noting the baseline prothrombin time before initiating oral anticoagulation and describes how well tolerated anticoagulation can be achieved in a patient with congenital factor VII deficiency.