Nano sized hydroxyapatites with silicon substitution of three different silicon concentrations were successfully prepared first time by a rapid microwave assisted synthesis method, with a time saving and energy efficient technique. The effects of the Si substitution on crystallite size, particle size and morphology of the powders were investigated. The crystalline phase, microstructure, chemical composition, and morphology and particle size of hydroxyapatite and silicon substituted hydroxyapatites were characterized by X-ray diffraction, Fourier transform infrared spectroscopy, scanning electron microscopy and dynamic light scattering. The crystallite size and particle size decreases with increase in silicon content and particle morphology spheroidal for pure hydroxyapatite changes to elongated ellipsoidal crystals while silicon substitution increases. Fourier Transform Infrared Spectroscopy analysis reveals, the silicon incorporation to hydroxyapatite lattice occurs via substitution of silicate groups for phosphate groups. Substitution of phosphate group by silicate in the apatite structure results in a small increase in the lattice parameters in both a-axis and c-axis of the unit cell.