Purpose: To elucidate the process of urinary stone formation, many urinary constituents have been examined as inhibitors or promoters. Materials and Methods: We analyzed specific binding proteins of calcium phosphate (CAP) crystals generated in human urine and found that the separated proteins were α2-HS-glycoprotein, prothrombin fragment 1 (PTF1), and osteopontin (OPN). We also studied their inhibitory effects on calcium oxalate crystallization and the quantitative differences in urinary excretion of the proteins in healthy individuals and stone formers. Results: Both PTF1 and OPN had strong inhibitory effects on growth of calcium oxalate crystals. No differences in α2-HS-glycoprotein were found between healthy subjects and stone formers. Urinary concentrations of PTF1 and OPN were lower in stone formers than in healthy controls. No differences in these proteins were seen between single and recurrent stone formers. Conclusion: Low urinary concentrations of PTF1 and OPN might be one reason for stone formation.