In the present study, we reviewed 73 Chinese cases of gastrointestinal stromal tumor (GIST), and analyzed factors in evaluating malignant potential, in particular focusing on Ki-67 index and p53 expression to determine whether these can be used as prognostic indicators in GIST. The p53 positive rate was 50.7% and it was significantly higher in malignant (25/35; 71.43%) than in benign cases (13/38; 34.21%). A Ki-67 labeling index of >10% was also significantly different between malignant (23/35; 65.71%) and benign cases (14/38; 36.84%). In the cases in which the patient died, 15/21 and 14/21 cases showed expression of p53 and Ki-67, respectively; both had a higher expression than in surviving cases. Comparing the cases positive for both Ki-67 and p53 with those positive for Ki-67 or p53 alone, and those negative for both Ki-67 and p53, the latter demonstrated the best prognosis. The study also indicated that the malignant potential of GIST is correlated with the mitotic index (> or =1/10 high-power fields; HPF), tumor size (> or =5 cm), high cellularity, tumor invasive growth, tumor location, tumor hemorrhage and tumor necrosis.