Objective To study the diagnosis, pathomorphological and immunohistochemical features of gastrointestinal stromal tumor (GIST) and to explore the reference parameters for malignancy. Methods Light microscopy was used to study the morphologic characteristics in 54 cases of gastrointestinal mesenchymal tumors, and the expression of CD117,CD34 and S 100 was detected by EnVision immunohistochemical method. ResultsMost borderline and malignant tumors were found in male. CD117 showed diffuse strong expression, CD34 mostly showed diffuse strong expression, S 100 incidentally showed focal expression, and the positive rates were 100%, 59% and 16% respectively. Conclusions CD117 is a sensitive and specific marker for the diagnosis of GIST. Tumor necrosis, high tumor cellularity and intestinal tumor mitotic activity over 1/50HPF were helpful parameters for judgement of malignancy, tumors are most often seen in male.