The present brief review focuses on the features of the Layer-by-Layer (LbL) synthesis of coatings containing hydroxyapatite nanoparticles and assesses their use in solving several biomedical problems. This work provides the state-of-art of this field. This method is based on the sequential chemical adsorption of reagents on the substrate surface that makes it possible to apply nanolayers of the specified composition on the surface of a wide range of substrates of complex shape, to control the thickness of the synthesized layers accurately at the nanometer level. It also enables the modification of surface characteristics, including roughness, hydrophilicity, and surface charge, and allows “artificially” constructed multilayers consisting of hybrid organic and inorganic substances to be obtained. The experimental material presented in the review demonstrates the effectiveness of LbL synthesis for creating new 3D scaffolds as bone substitutes, coatings on the surface of metal implants, and drug delivery systems. A promising direction for the development of LbL synthesis is the creation of methods that involve ion-substituted hydroxyapatites as reagents. Success in this area can pave the way for significant advances in biomedicine and open new opportunities for creating a new generation of structures that mimic the structural, compositional, and mechanical properties of the bone mineral phase.