High-resolution transmission electron microscopy (HRTEM), electron microdiffraction, and X-ray diffraction were used to study hydroxyapatite specimens with particle sizes from a few nanometers to several hundreds of nanometers. Diffuse scattering (without clear reflections in transmission diffraction patterns) or strongly broadened peaks in X-ray diffraction patterns are characteristic for agglomerated hydroxyapatite nanocrystals. However, HRTEM and microdiffraction showed that this cannot be considered as an indication of the amorphous state of the matter but rather as the demonstration of size effect and the morphological and structural features of hydroxyapatite nanocrystals.