The mechanical deformation of crystalline silicon induced by micro-indentation has been studied. Indentations were made using a variety of loading conditions. The effects on the final deformation microstructure of the load–unload rates and both spherical and pointed (Berkovich) indenters were investigated at maximum loads of up to 250 mN. The mechanically deformed regions were then examined using cross-sectional transmission electron microscopy (XTEM), Raman spectroscopy, and atomic force microscopy. High-pressure phases (Si-XII and Si-III) and amorphous silicon have been identified in the deformation microstructure of both pointed and spherical indentations. Amorphous Si was observed using XTEM in indentations made by the partial load–unload method, which involves a fast pressure release on final unloading. Loading to the same maximum load using the continuous load cycle, with an approximately four times slower final unloading rate, produced a mixture of Si-XII and Si-III. Slip was observed for all loading conditions, regardless of whether the maximum load exceeded that required to induce “pop-in” and occurs on the {111} planes. Phase transformed material was found in the region directly under the indenter which corresponds to the region of greatest hydrostatic pressure for spherical indentation. Slip is thought to be nucleated from the region of high shear stress under the indenter.