Snail, a zinc finger structure transcription inhibitory factor, has been reported to play an important role in the metastatic progression of several types of cancer. The aim of the study was to identify potential biomarkers for metastasis in gastrointestinal stromal tumors (GISTs) by examining the expression levels of Snail, E-cadherin, and Vimentin in GISTs and investigate their clinical significance. The protein expression of Snail, E-cadherin, and Vimentin in 74 GIST specimens was detected by immunohistochemical analysis, and the correlation between expression levels and clinicopathological data was analyzed. Snail, E-cadherin, and Vimentin were positively expressed in 51.4% (38/74), 32.4% (24/74), and 68.9% (51/74) of GIST tissue samples, respectively. Snail protein expression was significantly higher in GISTs with distant metastasis compared with GISTs without distant metastasis (P<0.05). E-cadherin expression level was significantly lower in cases of GIST with distant metastasis compared with those without distant metastasis (P<0.05), whereas the expression level of Vimentin did not significantly change according to clinical and pathological characteristics (all P>0.05). Snail expression was significantly negatively correlated with E-cadherin expression (r's=-0.276, P=0.017) but not with Vimentin expression (r's=0.041, P=0.728) in GISTs. High Snail expression and low E-cadherin expression were significantly correlated with metastasis in GISTs, and Snail, because of positive correlation, is potentially a biomarker of GIST with distant metastasis.