The synthesis of hydroxyapatite nanoparticles is reported using a hydrothermal microemulsion technique with calcium nitrate tetrahydrate and diammonium hydrogen phosphate as precursors is reported. The advantage of this proposed technique over other previously reported techniques is that particles with controlled size and morphology can be obtained with a new microemulsion with cetyltrimethylammonium bromide (CTAB)/toluene/n-butanol/water as a nanoreactor. X-ray diffraction (XRD) analysis showed that the hydrothermal microemulsion produced powders with phase-pure hexagonal hydroxyapatite. Transmission electron microscopy (TEM) showed that nanoparticles with both defined and undefined shapes can be obtained. Hydroxyapatite nanoparticles with a typical hexagonal prism-like morphology were obtained when microemulsion parameters such as the water to surfactant molar ratio (W0) and the cosurfactant to surfactant molar ratio (P0) were adjusted to defined values. The effects of changes in microemulsion parameters (W0 and P0) on sizes calculated using both transmission electron microscopy (TEM) and dynamic light scattering (DLS) were also investigated; the observed trends are discussed in terms of the interaction between amphiphilic molecules and hydroxyapatite precursor ions at the water-oil (W/O) interfaces.