This case report was with regard to familial heparin cofactor II (HC II) deficiency. The patient was a 14-years-old female, having complaints of chest pain, fever and swelling of right lower extremity. Echocardiography and DSA showed a pediculated mass at the right ventricular outflow tract which highly suggested a ventricular myxoma. At surgery, a large pediculated thrombus was removed from the RV conus septum aun pulmonary valve. The mass was identified as thrombus by histological examination. Two months later, the RV thrombi recurred with additional pulmonary embolus to the left lung. HC II was discovered by hemo-coagulation tests. Her HC II antigen value was 48%, and 32% on repeat study. Her brother's HC II antigen value was 53%. At reoperation, small thrombi less than phi 10 mm, were removed from the RV outflow tract and pulmonary valve. Fresh frozen plasma was given and intravenous urokinase therapy was taken. She is doing well with therapy of oral warfarin, aspirin and ticlopidine for anticoagulation.