A 39-year-old man was referred to hospital with a rectal tumour and underwent gastrointestinal endoscopy and diagnostic imaging. The tumour had immunohistochemical characteristics for gastrointestinal stromal tumour (GIST). The differential diagnosis of GIST to adenocarcinoma is important to be aware of for the rectal multidisciplinary team. On suspicion of GIST, patients should be referred to a sarcoma centre. The diagnosis of rectal GIST can be suggested on MRI by the presence of a well-defined heterogeneously large mass with a necrotic center associated with a prominent extra-luminal component and hyperechoic appearance on ultrasound.