We recently proposed a theory of mechanism-based strain gradient (MSG) plasticity to account for the size dependence of plastic deformation at micron- and submicronlength scales. The MSG plasticity theory connects micron-scale plasticity to dislocation theories via a multiscale, hierarchical framework linking Taylor's dislocation hardening model to strain gradient plasticity. Here we show that the theory of MSG plasticity, when used to study micro-indentation, indeed reproduces the linear dependence observed in experiments, thus providing an important self-consistent check of the theory. The effects of pileup, sink-in, and the radius of indenter tip have been taken into account in the indentation model. In accomplishing this objective, we have generalized the MSG plasticity theory to include the elastic deformation in the hierarchical framework.