First-principles modeling combined with experimental methods were used to study hydroxyapatite in which Sr2+ is substituted for Ca2+. Detailed analyses of cation-oxygen bond distributions, cation-cation distances, and site 1-oxygen polyhedron twist angles were made in order to provide an atomic-scale interpretation of the observed structural modifications. Density functional theory periodic band-structure calculations indicate that the Ca2+ to Sr2+ substitution induces strong local distortion on the hydroxyapatite lattice: the nearest neighbor Sr-O bond structures in both cationic sites are comparable to pure SrHA, while Sr induces more distortion at site 2 than site 1. Infrared vibrational spectroscopy (FTIR) and extended X-ray absorption fine structure (EXAFS) analysis suggest increasing lattice disorder and loss of OH with increasing Sr content. Rietveld refinement of synchrotron X-ray diffraction patterns shows a preference for the Ca1 site at Sr concentrations below 1 at.%. The ideal statistical occupancy ratio Sr2/Sr1=1.5 is achieved for approximately 5 at.%; for higher Sr concentrations occupation of the Ca2 site is progressively preferred.