Small bowel duplications are congenital structures commonly lined by heterotopic gastric or pancreatic mucosa. Though benign in children, small bowel duplications have the potential for malignant degeneration in adulthood. Here, we present the first reported case of metastatic adenocarcinoma arising from a small bowel duplication lined by gastroesophageal mucosa. The cancer demonstrated overexpression of the HER2/neu oncoprotein and amplification of the HER2/neu gene. This represents the only report of HER2 overexpression in this type of lesion. The patient is being treated with traditional chemotherapeutic agents in addition to monoclonal antibody therapy directed at the HER2 protein, and has demonstrated a clinical benefit from treatment. This case demonstrates that the anatomic location of a mass may be distinct from its biological origin, and this difference may have important practical implications for diagnostic testing and treatment.