Objective: To investigate expressions of Notch1, Notch3 and Hes1in gastrointestinal stromal tumors(GIST) and their clinical significance. Methods: The tissue specimens of 48 cases of resected GIST and tissue specimens of gastrointestinal tissue adjacent to 48 cases of GIST were collected. The protein expressions of Notch1 and Notch3 along with the down-steam target gene Hes1 were determined by immunohistochemical staining, and the relations of each protein expression with the clinicopathologic factors of GIST patients were also analyzed. Results: IIn GIST tissue compared with its adjacent gastrointestinal tissue, the positive expression rate of either Notch1 (58.33% vs. 29.17%), Notch3 (97.97% vs. 35.47%) or Hes1 (35.47% vs. 10.42%) protein was significantly increased (all P<0.05). After comparison of the positive expression rate of each protein between or among groups of GIST patients stratified by gender, age, tumor site, tumor size and NIH risk classification, the results showed that Notch1 expression was significantly associated with NIHrisk classification (χ2=16.53, P=0.001), Notch3 expression was irrelevant to any of the above factors (all P>0.05) and Hes1 expression was significantly related to tumor size (χ2=7.78, P=0.02). Conclusion: The expressions of Notch signaling pathway related proteins are increased in GIST tissue, which may play an important role in the occurrence and development of GIST.