Hydroxyapatite nanoparticles (HAp NPs) bare and doped with cobalt, nickel or copper were obtained via hydrothermal synthesis method and fully characterized by X-ray diffraction, Raman spectroscopy, Fourier-transform infrared spectroscopy, transmission electron microscopy techniques. It was shown that doping impact the band gap. The density function theory (DFT) calculations were employed to investigate the electrical properties of the hydroxyapatite with usage of functionals in local density approximation (LDA) and generalized gradient approximation (GGA). Two approaches to quantum-chemical calculations within DFT were considered. The densities of states were calculated for as-prepared samples and study of correlation between the calculated and experimental values of band gap was carried out. Revealed patterns provide a new viewpoint on the choice of dopants for biocompatible pigments and scaffold materials with semiconductor properties.