Many GISTs do not at first cause the patient any unusual or unpleasant symptoms, so they are often quite large before they are discovered. Those tumours are often discovered during emergency surgery for unexpected perforation of the gastrointestinal tract and consequent bleeding.
The type of symptoms and when they first occur depends on the size and location of the tumour.

If the tumour is situated in the stomach or the duodenum, the first signs could be a feeling of fullness, pain, gastrointestinal haemorrhages (black stool) or nausea. Tumours in the small intestine often reach a noticeable size before the pressure they exert on other organs leads to pain, haemorrhages, or constipation. Tumours in the large intestine can cause blood in the stools, along with constipation. Primary tumours in the oesophagus can lead to difficulties in swallowing.