Background: Primary mesenchymal tumors of the gastrointestinal tract are a heterogeneous group of tumors with a wide clinical spectrum, of which gastrointestinal stromal tumors (GIST) typically occur in middle-aged to older individuals. This study evaluated the clinicopathological and morphological features of GIST of the intestinal tract. Methods: The study included 108 gastrointestinal and 13 extra-gastrointestinal stromal tumors involving the mesentry and retroperitoneum between January 1989 and July 2007. Immunohistochemical expression of CD117, CD34, SMA, Desmin, S100, and Ki-67 were studied. Results: GIST comprised 108 of 120 (90%) of the mesenchymal tumors. The tumor was located in the stomach in the majority (55%) of patients followed by small intestine (30%), retroperitoneum (7%) and the colorectum (4%). There was a significant correlation between tumor size and mitotic index, with larger tumors having higher mitotic index (p < 0.001). Mitotic index per 5 mm2 correlated with high cellularity (p < 0.001), presence of necrosis (p < 0.001) and presence of mucosal invasion (p = 0.01). Expression of CD117 was seen in 94%, CD34 in 59%, SMA in 41%, S-100 in 33%, and desmin in 4% of tumors. Conclusion: We found GIST to be the most common mesenchymal tumor of the gastrointestinal tract. © 2011 Indian Society of Gastroenterology.