Here, we report the Ki-67 Labeling Index, the expression of c-kit, p53, bcl-2, and apoptosis in 11 gastrointestinal stromal tumors (GISTs). The Ki-67 Labeling Index in the malignant GIST group was higher than that in the benign group. The Ki-67 Labeling Index in the p53-positive cases was higher than that in the p53-negative cases. The Ki-67 Labeling Index in the C-kit-positive group was higher than that in the C-kit-negative group. The bcl-2 expression was not correlated with potential malignancy. The apoptotic count in the bcl-2-positive cases was higher than that in the bcl-2-negative cases. The Ki-67 Labeling Index, the p53 overexpression, and the C-kit expression were useful in predicting the potential malignancy.