AIM: To investigate the clinicopathological features of gastrointestinal stromal tumor (GIST) and to study the reference indexes for malignancy.METHODS: Fifty-two cases of primary GIST were distinguished from a group of gastrointestinal mesenchymal tumors using a panel of antibodies such as CD117 and CD34 by immunohistochemical SP method.Their biological behaviors were analyzed using the expression of p21WAF1 and Bax in 52 cases of GIST.RESULTS: Grossly, the tumor size was between 1.5 cm and 13 cm (mean: 5.5 cm). Focal areas of hemorrhage,necrosis, or small cyst formation could be seen.Microscopically, the tumor was composed of spindle cells (20 cases), epithelioid cells (20 cases) and mixed cells (12 cases). Immunohistochemically, CD117 and CD34 showed diffuse strong positive expressions, the positive rates were 98.1% and 92.3%. SMA, S-100,NSE, NF and MBP showed focal positive expressions, the positive rates were 48.1%, 28.8%, 25%, 21.2% and 42.3% respectively. Vimentins were all positive desmin and CgA were all negative. In normal adult stomach and intestine, the immunoreactive staining for CD117 and CD34 showed immunoreactive interstitial cells of Cajal in myenteric neuroplexus. Among the 52 cases of GIST, 27were positive for p21WAF1 (51.9%), 29 for Bax (55.8%).The expression of p21WAF1 and Bax had no significent difference with the localization, size, histological subtype of GIST, but had a significent difference with the histological grade (P = 0.000, respectively). p21WAF1expression had a positive correlation to Bax expression (r = 0.461, P = 0.001, κ = 0.459).CONCLUSION: GIST has complicated arrangements and various cell types. Positivity of CD117 and CD34 is the most valuable factor in diagnosing GIST. Expression of p21WAF1 and Bax plays an important role in potential malignancy and malignancy rather than in benign GIST.p21WAF1 and Bax may be used as the markers in the assessment of GIST malignant potential.