A 77-year-old man with myelodysplastic syndrome suffered from duodenal perforation after undergoing endoscopic submucosal dissection (ESD) for treatment of duodenal cancer. He presented with hemorrhagic shock, peritonitis and disseminated intravascular coagulation (DIC), and received transfusions of red blood cells (RBC), fresh frozen plasma (FFP), γ-globulin and albumin (Alb). One month after the last RBC transfusion, prolonged thrombocytopenia was observed, and platelet concentrate (PC) was transfused. However, immediately after starting PC transfusion, he developed dyspnea, hypotension and rash, and was thus diagnosed as being in anaphylactic shock. Analysis of the patient's serum revealed absence of haptoglobin (Hp) and the presence of anti-Hp antibody. Further studies, using PCR detected Hpdel, yielded a diagnosis of congenital Hp deficiency. Thus, the anaphylactic shock was considered to have been induced by Hp in the transfused PC reacting with pre-existing anti-Hp antibodies. Thereafter, transfusions were safely carried out with the use of washed PC. Congenital Hp deficiency is relatively prevalent, and in such cases transfusions should be carried out using washed RBC, washed PC and congenital Hp deficiency donor derived FFP to avoid anaphylactic transfusion reactions. Transfusions would be even safer if production of congenital Hp deficiency donor derived PC were to be made available in the future.