Recently the origin of gastrointestinal stromal tumors (GISTs) is thought be the interstitial cells of Cajal or primitive stem cells. This study was performed to evaluate the roles of fine needle aspiration cytology (FNAC), cell block preparation, and immunohistochemistry in the diagnosis of GISTs. Nine cases of GIST in which FNAC was performed were included in this study. Cytologically, the tumor cells characteristically occurred in closely packed cohesive tissue fragments with high cellular density often in bloody background. The tumor cells often formed fascicles with parallel, side-by-side arrangements of the nuclei. Histologically, GISTs were highly cellular spindle or epithelioid tumor with basophilic appearance. Immunohistochemically, GISTs were c-kit positive in all of nine cases, CD34 positive in seven, focally SMA positive in two, and S-100 and GFAP negative in all. Both histologic and cell block sections showed the same histologic and immunohistochemical features. Cytomorphologically GISTs show a broad morphologic spectrum but rarely a significant nuclear pleomorphism and the assessment of malignant potential is difficult based on cytology alone. However, in the appropriate clinical and radiologic setting, a confident diagnosis of primary or metastatic GIST can be established by FNAC, cell block, and immunohistochemistry.