BACKGROUND: Over the past decade, gastrointestinal stromal tumours (GISTs) have served as a model for the application of tyrosine kinase inhibitors in the treatment of solid neoplasms. Operative and medical management of GISTs is rapidly evolving, but current guidelines appear restricted to basic non-organ-specific recommendations. METHODS: A PubMed search was made of the English literature from 1998 to 2008 for references containing the terms 'gastrointestinal stromal tumours' and 'surgery'. This paper reviews the various operative strategies so far reported for GISTs within the digestive tract. RESULTS: Many original procedures tailored to the specific characteristics of these rare sarcomas have been reported. GISTs exhibit distinct features, in particular an absence of metastases within locoregional lymph nodes. Operations requiring extended lymph node dissection, typically designed for adenocarcinomas, such as gastrectomy with extended lymph node dissection, Whipple's procedure and total mesorectum excision, are inappropriate for treating GISTs originating from the stomach, duodenum and rectum respectively. CONCLUSION: GISTs allow the possibility of performing oncologically adequate but limited (wedge; segmental) resections. Such surgery can be carried out in a variety of ways, such as open, laparoscopic, trans-sacral or endoscopic.