Zonula occludens-1 (ZO-1) is a membrane-scaffolding protein that plays an important role in maintaining tight-junction integrity, which is disrupted in many invasive cancers and intestinal diseases. However, the expression of ZO-1 in gastrointestinal stromal tumor (GIST) and its relationship with clinical characteristics of this disease remain poorly understood. In this study, immunohistochemical analysis using tissue microarray was employed to evaluate the expression of ZO-1 in GIST and to investigate the relationship between its expression and GIST prognosis. High ZO-1 expression was displayed in 71.8 % of GIST patients, which was related to tumor diameter (p < 0.05). The Kaplan-Meier method and log-rank test indicated that high ZO-1 expression, small tumor diameter, tumor position in the esophagus, and a borderline-to-intermediate tumor grade displayed significant correlations with longer survival of GIST patients. The data suggest that ZO-1 expression is correlated with malignant phenotypes of GIST and it may serve as a favorable prognostic factor for GIST. These results also support a role for ZO-1 as a tumor-suppressor gene in GIST.