Nanopowders of aluminum-substituted (0-20 mol %) hydroxyapatite (HA) with the average size of 40-60 nm were synthesized by the precipitation method from nitrate solutions. A series of samples were studied by various analytical tools to elucidate the peculiarities of Al introduction. Electron paramagnetic resonance and pulsed electron-nuclear double resonance data demonstrate that incorporation of Al resulted in a decrease in the concentration of impurity carbonate anions and lead to an increase in the number of protons in the distant environment of the impurity nitrogen species. Density functional theory calculations show that the Al3+ incorporation is accompanied by the local positional rearrangement and the distortion of anion channel geometry. An in vitro test conducted on MG-63 cells demonstrates the cytocompatibility and magnification of the surface matrix characteristics with Al doping.