The aim of this study was to develop and test a scoring system based on real-time ultrasonography (US), which is able to predict the healing of a bone defect filled with a bone graft substitute or cancellous bone graft. We implanted porous hydroxy-apatite (HA) ceramic blocks into a segmental defect in the tibia of 51 sheep; 14 sheep received autologous bone graft from the iliac crest. Follow-up times were 3, 6 and 12 months. With the exception of the 12-month animals, there was a minimum of 6 animals in each group. At the end of follow-up the tibiae were tested in torsion to failure. These results were correlated with radiographic and ultrasound scores measured on the same specimens. With the scoring system it was possible to describe the osseous integration of the HA ceramic or mineralisation of the cancellous bone graft. Sheep with ceramic implant that developed non-unions showed a significantly lower score than sheep with a sufficient implant integration. A significant correlation between these scores and the biomechanical results was found. We were able to define a cut-off within the scoring system which made the prediction of instability/non-union possible. In our model we were able to predict the osseous integration of HA ceramics and autologous cancellous bone grafts with the use of real-time ultrasound.