The inter-dependence of diffusion behavior and grain microstructure in amorphous silicon/polysilicon-on-single crystal silicon systems has been studied for rapid thermal and furnace annealing for P and BF2 implants. It is found that the changes of microstructure during annealing play a major role in determining the diffusion profiles in the substrate as well as in the polysilicon layer. For P doping, a drive-in diffusion results in a much larger grain microstructure for as-deposited amorphous silicon than for as-deposited polysilicon, which leads to the formation of shallower junctions in the substrate for the first case. For B doping, there is little difference in the final microstructure and junction depth between the two cases. The P and B junctions formed in the substrate are found to be laterally very uniform in spite of expected doping inhomogeneities due to polysilicon grain boundaries both for as-deposited amorphous silicon diffusion sources and for as-deposited polysilicon diffusion sources.