This review covers areas where our understanding of the mechanisms underlying nanoindentation has been increased by atomistic studies of the nanoindentation process. While such studies have been performed now for more than 20 years, recent investigations have demonstrated that the peculiar features of nanoplasticity generated during indentation can be analyzed in considerable detail by this technique. Topics covered include: nucleation of dislocations in ideal crystals, effect of surface orientation, effect of crystallography (fcc, bcc, hcp), effect of surface and bulk damage on plasticity, nanocrystalline samples, and multiple (sequential) indentation. In addition we discuss related features, such as the influence of tip geometry on the indentation and the role of adhesive forces, and how pre-existing plasticity affects nanoindentation.