The present work aims to examine the effect of silicon substitution on thermal and in-vitro dissolution properties of carbonated hydroxyapatite. Hydroxyapatite [Ca10(PO4)6(OH)2, HA], carbonate substituted hydroxyapatite [Ca10(PO4)6-x(CO3)x(OH)2, x=1, 1CHA] and carbonate, silicate co-substituted hydroxyapatite [Ca10(PO4)6-x-y(CO3)x(SiO4)y(OH)2, x=1,y=1, 1C1SiHA] nanoparticles were prepared by microwave synthesis method under identical processing conditions. The XRD results of HA, 1CHA and 1C1SiHA correspond to the standard hexagonal HA (JCPDS 9-432). The crystallite size and lattice strain of the synthesized powder particles were estimated by Williamson-Hall isotropic strain model (W-H ISM) from powder X-ray diffraction data. The dislocation density was calculated by Williamson-Smallman formula. The functional groups present in the as-synthesized powder particles were analyzed by Fourier transform infrared (FT-IR) spectroscopy method. The size and the morphology were examined using a transmission electron microscope (TEM). The in-vitro dissolution behaviour of the synthesized powder particles was studied by ethylenediamine tetra-acetic acid (EDTA) titrimetric method. The W-H ISM results confirm that the prepared powder particles of HA, 1CHA and 1C1SiHA are nanocrystalline with an average crystallite size of 40 nm, 36 nm and 32 nm, respectively. Thus the crystallite size of hydroxyapatite was observed to be decreased gradually with increase in substitutions as indicated by the least size for the 1C1SiHA. In addition, the XRD results of powders annealed at 900 °C for 2 h show the improved thermal stability of 1C1SiHA compared to 1CHA. The TEM results show rod-like shaped morphology for HA, near rod-like with modified edge morphology and increased agglomeration for 1CHA and needle-like shaped morphology for 1C1SiHA powder particles. The in-vitro dissolution study results show a gradual increase in the solubility of HA with carbonate and carbonate-silicate co-substitutions. The calculated microstructural parameters, namely, crystallite size, root mean squared strain and dislocation density were correlated with in-vitro dissolution behaviour of hydroxyapatites.