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150 cases of Brunner's gland hamartoma (BGH) have been reported in the literature. BGHs are benign and are thought not to cause bile obstruction.In this case report, a 60-year-old male is presented with unexplained obstructive jaundice who was also known for over 17 years with diffuse adenomatous hyperplasia of Brunner's glands in the duodenum. Despite the benign preoperative diagnosis, the choice of treatment was Whipple's procedure due to suspicion of a coexisting malignancy.Pathological analysis of the resection specimen revealed multiple BGHs and an adenocarcinoma of the papilla of Vater (PoV). Molecular pathology using loss of heterogeneity analysis was used to confirm that both were different entities.It is likely that previous reports of malignant degeneration of BGHs may actually have been cases involving the coexistence of a PoV adenocarcinoma. Physicians need to be alert when a patient presents with BGH accompanied with obstructive jaundice for simultaneously occurring PoV adenocarcinoma.