Natural biopolymers such as collagen and fibrin have been widely used in bone regenerative applications. Despite the frequent use, their comparative biological propertiesis are largely unknown. In a previous study, we found the superiority of fibrin to collagen in the adsorption of serum proteins and the proliferation and differentiation of cultured osteoblasts. In this study, we used an in vivo model to evaluate how effectively fibrin supports bone regeneration, as compared with collagen. Collagen and fibrin were placed in critical size defects made on rat calvarial bones. Compared with collagen, fibrin supported substantially more new bone tissue formation, which was confirmed by micro-CT measurement and histological analyses. The cells in the regenerative tissues of the fibrin-filled defects were immunostained strongly for Runx2, while collagen-placed defects were stained weakly. These in vivo results demonstrate that fibrin is superior to collagen in supporting bone regeneration.