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The influence of the charge state of ion implantation induced defects in SOI waveguides on the absorption of sub-bandgap wavelengths is described. It is found that waveguides pre-doped with boron absorb with significantly greater efficiency than those pre-doped with phosphorus. Following annealing at 300degC this difference is approximately 8 dBcm-1, while the intrinsic loss of the waveguides is limited to 2 dBcm-1. These results have significant ramifications for a number of integrated optical devices fabricated in silicon.