The incorporation of ions in the lattice of hydroxyapatite alters significantly its structure. Particularly, if anions such as trigonal borate units are accommodated in the lattice severe distortions must occur around the substitution site because of different geometric shape, electric charge and anion size. Solid-state NMR has been used to investigate this problem in detail for a hydroxyapatite sample synthesized by high temperature solid state reaction. The results clearly verify the existence of network distortions. Indeed, only about 1/3 of the total phosphate content forms crystalline hydroxyapatite (also found in XRD) whereas the residual amount is contained in two different phosphate sites with 31P chemical shifts of 5.5 ppm and 2.3 ppm, but broad resonances lines suggesting disorder. Furthermore, a novel proton signal at -0.6 ppm was found which is directly associated with the borate incorporation. No specific correlation of the two structurally different borate units with the two phosphate groups is found.