Background: Heparanase is involved in the pathology of many diseases. Results: Heparanase cleaves heparan sulfate (HS) oligosaccharides in either consecutive or gapped cleavage mode. Conclusion: The susceptibility of glycosidic linkage bonds to heparanase degradation is sensitive to the nonreducing end saccharide structure of the cleavage site. Significance: The results will help us to understand the pathophysiological effects of HS that arise from heparanase activity.