Objective Heparanase can specifically cleave carbohydrate chains of heparan sulphate proteoglycans, which is an important component of the extracellular matrix. This study was designed to investigate the expression of heparanase in patients with colorectal cancer, and to analyze its relationships with progression of the cancer and clinical prognosis. Methods Samples were collected from 36 patients with colorectal cancers from 2003 to 2004 in Peking Union Medical College Hospital, and were embeded by Paraffin and fresh-frozened. The expression of heparanase mRNA and its protein were measured by RT-PCR and immunohistochemistry. The relationships between these expressions and the clinicopathologic information (tumor invasion, tumor differentiation, lymph node involvement, accompanying with colorectal adenoma and 2-year survival) were also evaluated. Results The expressions of heparanase mRNA in colorectal cancer (19/31， 61.3%) were significantly higher than those in normal colorectal tissues (6.5%). The overexpressions in normal tissues were positively correlated to the incidence of adenoma in patients with colorectal cancer （r=0.352， P=0.024）. The result of immunohistochemistry also showed that heparanase mainly expressed in the vascular endothelium within cancer tissues and the peripheral invased region outside cancer tissues. The 2-year disease-free-survival in patients with negative heparanase expression (88.9%) was higher than that with positive heparanase expression (50.0%), but there was no significant difference （P=0.078）. Conclusion Heparanase overexpressed in colorectal cancer tissues, and thus it may take a role as an indicator for the formation and prognosis of colorectal cancer.