To improve the efficiency of osteogenic repair, we compared 3 types of round granular bone substitutes composed of hydroxyapatite (HA) in a single opened large pore covered by one or more thin shell structure, biphasic HA and tricalcium phosphate (TCP) in a compact granules with small uniform interconnected internal pores, and bioglass(BG) in a compact granules with hierarchical interconnected pores its bone repair efficiency by evaluation of cellular toxicity, cellular attachment and proliferation rate, and osteogenic supportive effect. They were nontoxic and revealed no noxious effect on cellular proliferation and osteoblastic differentiation. The cultured cells were most effectively proliferated on HA granular bone substitute surface. However, the bony repair of calvarial defects was most effective by BCP granular bone substitutes. The implanted BCP and HA granular bone substitutes showed excellent osteoconductive bone growth and favorable bone regeneration within 3 weeks compared to BG granular bone substitutes. All type granular bone substitutes were well incorporated into newly formed bone without foreign body reaction. Except for HA granular bone substitute, some implanted BG and BCP granular bone substitutes were partially resobed by TRAP positive multinucletated cells. These findings suggest that round granular biphasic calcium phosphate bone substitute structured with fully interconnected uniform sized internal pore might be a more promising bone substitute for small-sized none load-bearing bone defects.