Background: Gastrointestinal stromal tumor (GIST) is the most common mesenchymal neoplasm of the gastrointestinal tract. The expression of the epithelial markers in gastrointestinal stromal tumor is not frequently reported in the literature. The aim of this study was to investigate the immunohistochemical expression of several types of cytokeratins in GISTs and to correlate these findings with various parameters. Methods: Immunohistochemical staining for CKAE1, CKAE3,34 beta E12, CK5/6.CK7 and CK20 was carried out on paraffin embedded tissue sections of 4 mu m thick from specimen of 36 patients. Data about sex, age, tumor location and size, mitotic count, depth of invasion, ki67 antigen, cell proliferation index and risk of aggressive behavior were obtained from all patients. Cases were classified in four group corresponding to the percentage of positive cells in each marker (score): 0: negative, 1:<10%, 2: 10-50%, 3:>50%. Results: All 36 cases revealed no expression of cytokeratins 5/6,20,34 beta E12 and CKAE1. The expression of CK7 was observed in 2 (5,5%) cases and 3 (8,3%) cases showed CKAE3 expression. The expression of the latest cytokeratins was less than 10% in all cases. No significant statistical association was found between CKAE3 and CK7 immunoreactivity and several clinicopathologic parameters, including sex, age, tumor location and size, mitotic count, depth of invasion, ki67 antigen and risk of aggressive behavior. Conclusion: Although rare GISTs may express CK immunomarkers, but caution is necessary to avoid an erroneous diagnosis of a carcinoma or a neuroendocrine tumor.