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Abstract Background Intussusception in adult patient is rare. Gastroduodenal intussusception due to the gastrointestinal stromal tumors is infrequently described in the literature. Authors present a case of gastroduodenal intussusception due to the low-risk gastrointestinal stromal tumor of the lesser curvature of the gastric body with literature review. Case presentation Sixty-two-year-old male was admitted to our hospital with symptoms of acute gastric outlet obstruction. Imaging studies confirmed a lesion of the gastric wall producing gastroduodenal intussusception with pylorus obstruction. Upon laparotomy a tumor mass of the lesser curvature of the gastric body that invaginated through the pylorus into the duodenum was found. Desinvagination and resection of the tumor with the adequate resection margins were performed. Histology reveled a low-risk gastrointestinal stromal tumor. Due to favorable outcome only observation was suggested by the multidisciplinary team. Conclusions Gastroduodenal intussusception due to the gastrointestinal stromal tumor of the gastric wall is a rare event. Surgical resection is the treatment of choice. In selected cases laparosopic resection of the tumor can be performed.