Endostatin is a potent angiogenesis inhibitor with heparin-dependent activities. Nucleolin, a novel functional receptor of endostatin, mediates both the internalization to endothelial cells and the antiangiogenic activity of endostatin. To define the exact role of the heparin binding motif in mediating the interaction between endostatin and its receptor nucleolin, up to six arginine residues (R155, R158, R184, R270, R193, and R194) located in the heparin binding motif of endostatin were substituted by alanine to make double, quadruple, or hexad point mutations, respectively. Contributions of the heparin binding motif to both the interaction with nucleolin and the biological activities of endostatin were investigated from in vitro to in vivo. Here we show that Arg to Ala point mutagenesis of the heparin binding motif does not interrupt the folding of endostatin but significantly impairs the interaction between endostatin and nucleolin. Double and quadruple mutants showed significantly decreased internalization to endothelial cells and antitumor activities, while the hexad Arg to Ala mutant completely lost its interaction with nucleolin and biological functions. Taken together, the present study demonstrates that the arginine clusters in the heparin binding motif of endostatin significantly contribute to its interaction with receptor nucleolin and mediate the antiangiogenic and antitumor activities of endostatin.