A Transmission Electron Microscopy study of the defect microstructure in Silicon On Sapphire before and after Rapid Thermal Annealing is presented. The annealed material is shown to contain a much lower density of twins and threading dislocations. Comparison with the asgrown microstructure enables possible explanations to be proposed for these observations in terms of the removal of barriers to the introduction and movement of dislocations in response to misfit and thermal expansion strains. A regular array of misfit dislocations is observed in the interface of annealed material. These have non-rational line directions and are consistent with complete misfit accommodation.