We report an unusual case of Brunner gland hamartoma of the duodenal bulb with multiple ciliated cysts in a 43-year-old man. The patient presented with regurgitation. An endoscopy of the upper digestive tract revealed the presence of a pedunculated tumor of the first duodenum. Surgical resection of the antrum and first duodenum was performed. The polypoid lesion measured 3.5 cm and was located in the submucosa. It was composed of predominant adipose tissue containing hyperplastic lobules of Brunner gland and cystic ducts lined by ciliated cells. Brunner gland hamartoma is a rare benign duodenal lesion; it is usually composed of mature but disorganized tissues and is found most commonly in the duodenum. The presence of ciliated cells in the gut mucosa is a rare phenomenon, which has already been described in the esophagus and stomach. We report an unusual case of ciliated metaplasia in a duodenal Brunner gland hamartoma.