Objective: A nationwide database was performed for gastrointestinal stromal tumors (GISTs) in a large series of primary GISTs surgically treated at centers all around Turkey. The aim of this multicenter study was to analyze and compare the performance of the National Institute of Health (NIH) and Armed Forces Institute of Pathology (AFIP) risk criteria to determine the ideal risk stratification system. Method: Statistical analysis of a nationwide database is consisted of age, gender, location, risk groups, histopathologic features and the results of CD117, CD34, Desmin, SM Actin, S-100 protein, and Ki67 immunohistochemistry. Results: In 1965 cases registered in database, male to female ratio was 1.20 and mean age was 57.64 years. Most common location was stomach (47.5 %) followed by small intestine, omentum-peritoneum, large intestine, and esophagus (30.3 %, 12.1 %, 9.1 %, 1.0 % respectively). Comparison of the two risk-stratification systems demonstrated that proposed modified AFIP seems to be better when compared with NIH system. Many histopathologic and immunohistochemical findings showed significant correlation with risk groups of AFIP, even with 'not sufficient data' group (p<0.005).