The optical properties of hydroxyapatites (HAps) and bio HAps have been studied using Raman and infrared (IR) spectroscopies to describe their crystalline quality. However, the size of the HAp crystals and their crystalline order effects have not been considered yet. This paper focuses on the study of the effect of the change in the crystallites size have on the width of the IR and Raman spectra for defatted and deproteinized bones as well as incinerated biogenic HAp obtained from bovine, porcine, and human bones. Bone samples were analyzed through Raman and IR spectroscopies, X‐ray diffraction (XRD), transmission electron microscopy (TEM), inductively coupled plasma (ICP), and scanning electron microscopy (SEM). The Raman and IR spectra for raw samples showed broad bands but, after calcination at 720 °C, became narrow and well defined. TEM images showed that all raw crystallites are ordered nanoplates contrary to the so far well‐established concept that biogenic HAps have low crystalline quality. XRD data confirmed that raw samples display broad peaks that correlated with the HRTEM images of ordered nanocrystals. This fact confirmed that the broad Raman and IR bands of raw clean bones come from nanocrystal plates. SEM analysis confirmed the increase in the crystal size after calcination from nanomicron to submicron dimensions due to a coalescence phenomenon. These results imply that the interpretation of Raman and IR spectra in the case of HAp nanoparticles has been erroneous. These results contribute to the design of biomaterials for tissue engineering based on biogenic HAp for bone regeneration.