Defects produced by ion implantation in Si and Ge, their evolution upon post-implantation annealing, and their role in shallow junction formation processes in Si and Ge are reviewed in this chapter. After summarizing the main mechanisms underlying the defect generation and accumulation during the ion implantation processes, the damage evolution during post-implantation annealing will be treated, with emphasis on agglomerates of intrinsic defects in Si. Afterward, anomalous dopant diffusion and electrical activation phenomena occurring in Si and Ge after post-implantation annealing will be treated, with a particular focus on point defect engineering strategies for shallow junction optimization.