Nanoindentation is a well-stablished experiment to study the mechanical properties of materials at the small length scales of micro and nano. Unlike the conventional indentation experiments, the nanoindentation response of the material depends on the corresponding length scales, such as indentation depth, which is commonly termed the size effect. In the current work, first, the conventional experimental observations and theoretical models of the size effect during nanoindentation are reviewed in the case of crystalline metals, which are the focus of the current work. Next, the recent advancements in the visualization of the dislocation structure during the nanoindentation experiment is discussed, and the observed underlying mechanisms of the size effect are addressed. Finally, the recent computer simulations using molecular dynamics are reviewed as a powerful tool to investigate the nanoindentation experiment and its governing mechanisms of the size effect.