Heparanase is endoglycosidase that degrades heparan sulfate, the main polysaccharide constituent of the extracellular matrix and basement membrane. Heparanase has been thought to have an important role in the process of cancer invasion and metastasis. Recent studies have revealed that heparanase has multifunctional modulatory effects in the progression of cancer cells and the cell-to-extracellular matrix interaction. Our recent research has shown the important roles of heparanase in the progression of esophagus, stomach and colon cancer, and heparanase expression was closely related to the prognosis of gastrointestinal cancer. Therapies targeting heparanase may result in promising tactics in cancer therapies. Heparanase gene silencing and inhibiton of enzymatic activities have potential use as targets for anticancer drug development. Here, we reviewed the role of heparanase in gastrointestinal tract tumors.