Duplication cysts are rare congenital anomalies of the gastrointestinal tract and the occurrence of multiple such cysts is an extremely rare occurrence. Autoimmune hemolytic anemia is an extremely unusual manifestation of these duplication cysts. Herein, we report a case with two duplication cysts (one cyst in the thorax; another in the abdomen) complicated with autoimmune hemolytic anemia. This patient was a five year-old-male child who presented with congestive cardiac failure due to severe anemia (which, on evaluation, was diagnosed as autoimmune hemolytic anemia). Imaging studies (chest radiograph and
computed tomography) revealed duplication cysts in the chest and abdomen. Anemia flare-up was noted in the patient despite two months of prednisolone therapy (2 mg/kg/day) and two high dose intravenous methylprednisolone pulse therapy courses (30 mg/kg/day for 5 days each). The steroid refractory autoimmune hemolytic anemia responded to rituximab (375 mg/ m2 body surface area/week for 4 weeks). Four months after tapering off the steroid therapy, the patient did not experience flare-up of the anemia. To the best of our knowledge, this is the youngest and first pediatric age group patient to be reported, with a possible association between gastrointestinal duplication cysts with autoimmune hemolytic anemia.