Primary intestinal lymphangiectasia (PIL) is a rare disorder characterized by dilated intestinal lacteals that result in leakage of excessive serum proteins and lymphocytes into the gastrointestinal (GI) tract culminating in protein-losing enteropathy. The GI loss of protein and possible antithrombin III (AT-III) loss creates a prothrombotic environment. The surgical management of congenital heart disease (CHD) in presence of PIL can present with altered heparin response and can impose problems in instituting cardiopulmonary bypass (CPB). We report a case of surgical closure of ventricular septal defect with PIL with altered heparin response. Such an association of PIL with altered heparin response in CHD has not been reported in literature.