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The formation of shallow junctions in germanium substrates, compatible with deep submicron CMOS processing is discussed with respect to dopant diffusion and activation and damage removal. Examples will be discussed for B and Ga and for P and As, as typical p- and n-type dopants, respectively. While 1 to 60 s Rapid Thermal Annealing at temperatures in the range 400-650oC have been utilized, in most cases, no residual extended defects have been observed by RBS and TEM. It is shown that 100% activation of B can be achieved in combination with a Ge pre-amorphisation implant. Full activation of a P-implant can also be obtained for low-dose implantations, corresponding with immobile profiles. On the other hand, for a dose above the threshold for amorphisation, a concentration-enhanced diffusion of P occurs, while a lower percentage of activation is observed. At the same time, dose loss by P out-diffusion occurs, which can be limited by employing a SiO2 cap layer.