Ab initio density functional plane-wave calculations are performed on silicon-substituted hydroxyapatite (SiHA). Formation energies are obtained for the substitution of a phosphorus atom by a silicon atom in each of the six phosphate groups of the unit cell in turn. It is found that the co-removal of a hydroxyl group to maintain charge neutrality is energetically favourable and the calculated unit cell volumes for the single silicon substitutions agree extremely well with experimental observation. The substitution of a second silicon atom in the unit cell is found to be almost as energetically favourable as the first (and on one site more favourable) and there can be an attractive interaction between the two Si substituents when they are closely separated. However, experimental observation suggests that for this concentration of silicon a phase transformation to a different structure occurs which, because of the imposed boundary conditions, could not be accessed in the calculations. The density of states of the SiHA indicates that new states are introduced deep into the valence band and the band gap decreases by 1.6 eV compared to phase-pure HA. No new states are introduced into the band gap indicating that the Si incorporation does not make the material inherently electrically active. Furthermore a population analysis shows that the Si impurity has only a small effect on the neighbouring ionic charge.