Abstract The osseous response to silicon (Si) level (0, 0.2, 0.4, 0.8 and 1.5 wt% Si) within 5 batches of matched porosity silicate-substituted hydroxyapatite (SA) scaffold was assessed by implantation of 4.6 mm diameter cylinders in the femoral intercondylar notch of New Zealand White rabbits for periods of 1, 3, 6 and 12 weeks. Histological evaluation and histomorphometric quantification of bone ingrowth and mineral apposition rate (MAR) demonstrated the benefits to early (<1 week) bone ingrowth and repair through incorporation of Si, at all levels, in porous hydroxyapatite (HA) lattices as compared to stoichiometric (0 wt% Si) HA. The group containing 0.8 wt% Si supported significantly more bone ingrowth than all other groups at 3 and 6 weeks ( P < 0.05 ), initially through its elevated MAR between weeks 1 and 2, which was significantly higher than that of all other Si-containing groups ( P < 0.05 ). The level of silicate substitution also influenced the morphology and stability of the repair, with elevated levels of bone resorption and apposition apparent within other Si-containing groups at timepoints >3 weeks as compared to the 0 and 0.8 wt% Si groups. At 12 weeks, the net amount of bone ingrowth continued to rise in the 0, 0.8 and 1.5 wt% groups, apparently as a result of adaptive remodelling throughout the scaffold. Ingrowth levels remained highest in the 0.8 wt% Si group, was characterised by a dense trabecular morphology in the superficial region graduating to a more open network in the deep zone. These results highlight the sensitivity of healing response to Si level and suggest that an optimal response is obtained when SA is substituted with 0.8 wt% Si through its effect on the activity of both bone forming and bone resorbing cells.