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The aim of this work was to examine the dependence of the local surface structure (surface structural heterogeneity) on the local thickness (thickness uniformity) and structure properties along the thickness of hydroxyapatite coatings (HACs) deposited by using the high power (52 kW) laminar plasma jet. For the deposition process, a relatively small size of the feedstock hydroxyapatite powder (HAP) (33 mu m) was used. The HACs were deposited at different stand-off distances (SODs) (80, 100, and 150 mm) without preheating of substrates. The thickness measurements were performed by using the calibrated micrometer and light microscopy (LM). The surface micro-structure was analyzed by using the micro-Raman spectroscopy (MRS), whereas the micro-structure along the thickness of HACs was studied by using the MRS, X-ray powder diffractometry (XRPD), and LM (combined with chemical etching). The results showed a heterogeneous phase distribution on the surface of each HAC analyzed as well as the non-uniform thickness of HACs. Apparently, a correlation existed between the local surface structure and the local thickness of HACs. However, the MRS, XRPD, and LM analyses of micro-structure along the thickness of HACs indicated that the differences in the local surface structure could be related to the different recrystallization established during the plasma deposition process in the different parts along the thickness of each HAC analyzed.