Abstract Theoretical and experimental investigations of the atomic and electronic structures of isomorphically substituted strontium apatite were carried out. The investigation was for the change in electronic structure of Sr5(PO4)3OH (Sr-HAP) at isomorphous substitution by F, Cl, and Sr by Na, La and also at transition Sr-HAP to amorphous state. Great changes were found in the binding energy of Sr core electrons at isomorphous substitution OH by F and Cl. It was shown that the binding energy of Sr 2p3/2-electrons in Sr-HAP is similar to the binding energy of Sr 2p3/2-electrons in SrCO3 at various binding energies of O 1s-electrons. Change in the half-width of P 2s-lines of the studied compounds may indicate decrease of the tetrahedron symmetry in the row of OH, Cl, F and at the same time practical coincidence of their positions and widths for Sr-HAP, and amorphous strontium hydroxyapatite may indicate conservation of tetrahedron symmetry and possible equal local atomic regulation. Isomorphous substitution of Sr-HAP by Na and La results in an increase in the binding energy of O and Sr core levels and at the same time a decrease in binding energy of P 2s-level, which indicates decrease of the electron density at P and increase of the electron density at O and Sr atoms. La and Na levels shifts to the region of high binding energies at transition from Sr5−2xNaxLax(PO4)3OH (x=0.25) to Sr5−2xNaxLax(PO4)3OH (x=1.0), which indicates that electron density transfers from matrix atoms to La and Na ones.