There are numerous causes of iron deficiency anemia due to gastrointestinal tract bleeding in children. While a very thorough history may elucidate common etiologies, such as cow's milk protein-induced colitis and nonsteroidal anti-inflammatory drug-related gastritis or peptic ulcer disease, other less frequent causes often present a diagnostic challenge. We present the MR enterography (MRE), CT and Meckel scan findings of ileal dysgenesis coexisting with multiple enteric duplication cysts in a young child who presented with chronic iron deficiency anemia, recurrent gastrointestinal tract bleeding and unexplained bowel perforation. In this case, MRE was able to identify and characterize each individual lesion and directly guide appropriate surgical management.