Hydroxyapatite (HA, Ca10(PO4)6(OH)2) is one of the most important biomaterials used in bone regeneration therapies due to their chemical properties are very similar to the inorganic phase found in bone tissues. The direct observation of the ultrastructure of HA is very important in the comprehension of their nucleation and interactions with the molecules involved in bone formation. High-resolution Transmission Electron Microscopy (HRTEM) is a currently technique used for this task. However, the interpretation of the images is not straightforward and needs the use of softwares dedicated to high-resolution images simulations. This work presents the applicability of MEGACELL software in the analysis of HRTEM images of HA nanoparticles. MEGACELL is the most newly software, developed to construct nanocrystals models for HRTEM multislice simulations. The output files generated by MEGACELL are raw data format (.xyz), containing all the atomic positions, as well as input files compatible with JEMS (Java Electron Microscopy Software) format files. High-resolution images were acquired using a JEM 3010 URP microscope, with a LaB6 thermionic electron gun operating at 300 kV, with a point-to-point resolution of 0.17 nm and a CCD Gatan 794SC multiscan digital camera, attached to the DigitalMicrographTM software for recording and image processing. Electron microscopy samples were prepared by dropping HA powder on copper TEM grids. HRTEM experimental images of HA particles, orientated along different zone axes, were interpreted applying the MEGACELL software to construct HA nanocrystal models and the multislice method to simulated them. MEGACELL improves the extraction of the ultrastructural features and facilitates a better interpretation of the phase-contrast images.