Experimental and theoretical investigations of nanoindentation into fcc silver and bcc iron were performed, including an investigation of the effect near the grain boundaries. Experimentally, micrograph images of the surfaces and force-depth curves were obtained which were used to determine the hardness and Young's modulus of the materials. Molecular dynamics simulations, on smaller systems than those investigated experimentally, exhibit the main experimental attributes, showing the plastic deformation of the substrates with piling-up of the work material along the indenter sides. The simulations also show how defects in the substrates form and these are contrasted with the various materials under investigation.