Gastrointestinal stromal tumour (GIST) is the designation used here to identify the most common subset of gastrointestinal mesenchymal tumours specific to those sites. These tumours have unique histological, immunophenotypic and molecular genetic features that set them apart from typical smooth muscle tumours and schwannomas; however, by tradition, they have been classified as GI-smooth muscle tumours, or stromal tumours/smooth muscle tumours. GISTs occur predominantly in persons over 40 years of age with an equal sex incidence. Benign GISTs outnumber the malignant ones by a margin of 10:1. GISTs occur throughout the gastrointestinal tract, but are most common in the stomach (60-70%) and small intestine (30%). GISTs are rare in esophagus, colon and rectum. Histologically they may show a spindle cell or epithelioid pattern (the former largely corresponds with the designation of cellular leiomyoma and the latter with that of leiomyoblastoma). Immunohistochemically most GISTs are positive for CD34 and c-kit protein (CD117); the latter is quite specific for GISTs among mesenchymal tumours. Genetically GISTs commonly show DNA losses in the long arm of chromosome 14, and c-kit gene mutations occur at least in some cases. c-kit is also expressed in the interstitial cells of Cajal, the gastrointestinal pacemaker cells, and relationship of GISTs to these cells has been proposed recently. GISTs differ histologically, immunohistochemically and genetically from typical (esophageal) leiomyomas that are negative for c-kit and CD34 and neither show DNA-losses in 14q nor c-kit mutations. Evaluation of malignancy of GISTs is based on mitotic count, tumour size and extra-gastrointestinal spread. Tumours with mitotic counts higher than 5/10 high power fields or larger than 10 cm have a significant risk for recurrence and metastasis and are considered histologically malignant; however, some tumours with mitotic activity < 1/10HPF may metastasize indicating some uncertainty in malignant potential of GISTs, especially those larger than 5 cm.