The aim of this study is to analyze the clinical outcome of gastrointestinal stromal tumors (GISTs) and to determine new prognostic factors. We perform a retrospective study of all the patients diagnosed with GIST in any location and operated on between 2000 and 2008 at our institution. We analyzed 35 patients, 16 males (45.7%) and 19 females (54.3%), with a mean age of 64 +/- 13.8 years. The tumors were located in the stomach in 22 patients (62.9%), in the small bowel in 10 (28.6%), and the retroperitoneum in three (8.6%). Referring to gastric GIST, endoscopy revealed an ulceration in the mucosa in five cases, suggesting an epithelial neoplasm. In all these cases, pathology of the biopsy specimen was nonconclusive. Survival rate at 1 and 5 years was 94.3 and 88.6 per cent, respectively. Disease-free survival at 1 and 2 years was 91.4 and 88.6 per cent, respectively. Analyzing prognostic factors, a lower disease-free survival was observed among patients with constitutional syndrome at diagnosis (P = 0.000), small bowel GIST (P = 0.037), and tumors not expressing actin (P = 0.015). A lower global survival was observed among men (P = 0,036), patients with an abdominal mass (P = 0.033) or with constitutional syndrome (P = 0.007) at diagnosis and tumors at a retroperitoneal location (P = 0.0002). Gastric GIST may be confused with epithelial neoplasms, modifying the surgery. In our patients, masculine gender, constitutional syndrome and abdominal mass at diagnosis, small bowel and retroperitoneal location, and actin negative tumors are bad prognostic factors.