BackgroundGastrointestinal stromal tumors are the most common mesenchymal neoplasms affecting the gastrointestinal tract. The stomach is the most common location to be affected, and the rectum one of the rarest, but the whole gastrointestinal tract remains susceptible. Gastrointestinal stromal tumors account for only 0.1% of rectal tumors. Currently, endoscopic ultrasound plays an essential role in the diagnostic process of gastrointestinal stromal tumors, especially when the affected sites have a worse outcome and higher morbidity rates.Case presentationWe describe the case of a 68-year-old white Japanese man with a history of long-term mild rectal pain and tenesmus. A digital rectal examination revealed a right palpable solid mass ranging from 3 to 7 cm from his anal verge. A colonoscopy was performed and showed a 5 cm elevated lesion covered by normal mucosa, located 4 cm above the pectineal line. Endoscopic ultrasound confirmed the diagnosis of a homogeneous hypoechoic mass with areas of necrosis as a rectal subepithelial lesion originating at the fourth layer (muscularis propria). He then underwent endoscopic ultrasound-guided fine needle aspiration of the lesion, followed by cytological and immunohistochemistry evaluation. The evaluation showed spindle and epithelioid cells of variable sizes, in fascicles separated by stroma, which reacted firmly and consistently to CD117/c-kit and CD34, and negative to desmin and S-100 protein. There was weak staining for nuclear Ki-67 in the tumor cells. A diagnosis of rectal gastrointestinal stromal tumor was confirmed. After a multidisciplinary meeting, an abdominoperineal resection of his rectum was performed. The pathology of the specimen confirmed the diagnosis of rectal gastrointestinal stromal tumor. He is now asymptomatic after 3 months’ follow-up and is on adjuvant therapy with a tyrosine-kinase inhibitor.ConclusionsGastrointestinal stromal tumors are rare tumors, and among the variety of primary location sites, the rectum is one of the rarest. The localization of this type of tumor has worse outcomes and higher morbidity rates. We report this rare case to emphasize the need for precise diagnosis and the important role of endoscopic ultrasound-guided fine needle aspiration in such situations.