Hydroxyapatite is one of the building blocks of hard tissues of living organisms. Therefore stability of nanoparticles in experimental solutions of different pH similar to one in human body is important issue for precise tailoring of the synthesis of hydroxyapatite particles on clay mineral substrate. In this study, the stability (amount of CaII and PV released into the water) of calcium deficient hydroxyapatite/clay mineral nanocomposites was investigated. The calcium deficient hydroxyapatite/clay mineral nanocomposites with montmorillonite and two vermiculites (Brazil and Bulgaria) were compared with pure calcium deficient hydroxyapatite. The stability was investigated for 24 h where calcium deficient hydroxyapatite/clay mineral nanocomposites and pure calcium deficient hydroxyapatite were placed into the water solutions with different pH values (pH= 5, 7, and 9). The presence of CaII and PV ions at solutions were determined using atomic emission spectrometry. The calcium deficient hydroxyapatite/clay mineral nanocomposites after stability testing were characterized by X-ray powder diffraction and infrared spectroscopy with Fourier transformation.