Structures of some bisphosphonates (clodronate, etidronate, pamidronate, alendronate, risedronate, zoledronate) were relaxed and analyzed by DFT method. By comparing their adsorption energies onto hydroxyapatite (001) surface with and without solvation effect and analyzing HOMOs (highest occupied molecular orbitals), LUMOs (lowest unoccupied molecular orbitals), and DOS (density of states) of bisphosphonates and hydroxyapatite (001) surface, it can be shown that the binding affinity of alkyl N-BPs (bisphosphonates containing nitrogen atom in an alkyl chain) is the highest among bisphosphonates, and the adsorption energy of bisphosphonates onto hydroxyapatite (001) surface is the main factor to determine the binding affinity of bisphosphoates with bone material.