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AIM: To explore the relationship between clinicobiological behavior and the expression levels of telomerase activity,apoptosis, p53 gene and bcl-2 gene in gastrointestinal stromal tumors (GISTs).METHODS: The intensity of telomerase activity,apoptosis, p53 and bcl-2 expression in GISTs were detected by telomeric repeat amplification protocol, in situ end-labeling technique, and immunohistochemistry,respectively.RESULTS: The positive rates of telomerase activity of malignant GIST, potential malignant GIST and benign GIST were 85% (17/20), 22.8% (2/9) and 0 (0/9),respectively. The apoptosis indices of malignant GIST,potential malignant GIST, and benign GIST were 11.7 ± 5.4, 30.2 ± 5.6 and 45.2 ± 7.2, respectively. The intensity of telomerase activity and apoptosis were related to the biological characteristics of GISTs (85% vs 22.8%, 0, 0; P ＜ 0.01 or 11.7±5.4 vs 30.2 ± 5.6, 45.2 ± 7.2, 72.1 ± 9.3; P ＜ 0.05). The intensity of telomerase activity was negatively correlated with cellular apoptosis (22.9 ± 8.4 vs 9.5 ± 5.7, P ＜ 0.01). The intensity of telomerase activity was positively correlated with p53,bcl-2 expression (40.0% vs 78.9%, 40.0% vs 84.2%;P ＜ 0.05).CONCLUSION: The detection of telomerase activity,apoptosis and its control genes in GIST will be helpful for the discrimination of the malignant and benign GIST and evaluation of the prognosis.