Hydroxyapatite (HA) is important in biomedical applications because of its chemical similarity to the mineral content of bone and its consequent bioactivity. Silicon substitution into the hydroxyapatite crystal lattice was found to enhance its bioactivity both in vitro and in vivo [1, 2]. However, the mechanism for the enhancement is still not well understood. In this paper, the crystal imperfections introduced by silicon substitution were studied using XRD and Raman spectroscopy. It was found that silicon substitution did not introduce microstrain, but deceased the crystal size in the hk0 direction. Three new vibration modes and peak broadening were observed in Raman spectra following silicon incorporation. The imperfections introduced by silicon substitution may play a role in enhancing bioactivity. A phenomenological relationship between the width of the PO4 v1 peak and crystal size was established.