In the past 5 years, there has been a paradigm shift in our understanding of gastrointestinal stromal tumors (GISTs). Once thought to be smooth muscle tumors, these uncommon neoplasms are now thought to differentiate along the lines of interstitial cells of Cajal, the pacemaker cells of the gut. Along with this understanding comes an exciting new drug therapy (Gleevec) that for the first time offers real hope to patients with malignant stromal tumors. Overall, approximately 60 -70% of stromal tumors are from the stomach, 20 -30% are from the small intestine, and <10% come from the esophagus, colon, rectum, omentum, and mesentery. Between 10 and 30% of GISTs are malignant. Stromal tumors should be studied in a site-specific fashion, as tumors from a given location in the gut have unique growth patterns and corresponding behaviors. Although the most important tool needed to diagnose a GIST is still a hematoxylin and eosinstained section, a confirmatory CD117 stain is recommended (and may be required for drug therapy). True smooth muscle tumors, inflammatory fibroid polyps, fibromatoses, schwannomas, inflammatory myofibroblastic tumors, and solitary fibrous tumors all enter into the differential diagnosis of GISTs. This article reviews the histologic features of these tumors in the context of recent molecular genetic and immunohistochemical advances.