The nanoindentation behaviour and phase transformation of annealed single-crystal silicon wafers were examined. The silicon specimens were annealed at temperatures of 250, 350 and 450°C, respectively, for 15 min and were then indented to maximum loads of 30, 50 and 70 mN. The phase changes induced in the indented specimens were observed using transmission electron microscopy (TEM) and micro-Raman scattering spectroscopy (RSS). For all annealing temperatures, an elbow feature was observed in the unloading curve following indentation to a maximum load of 30 mN. Under higher loads of 50 mN and 70 mN, respectively, the elbow feature was replaced by a pop-out event. The elbow feature reveals a complete amorphous phase transformation within the indented zone, whereas the pop-out event indicates the formation of crystalline Si XII and Si III phases. The formation of these phases increased with an increasing annealing temperature and indentation load. Moreover, the hardness and Young's modulus both decreased as the annealing temperature and indentation load increased. For the specimens annealed at 450°C and then indented to maximum loads of 50 mN and 70 mN, respectively, micro-cracks initiated at the bottom of the phase transformation region and extended into the silicon substrate. In other words, under high annealing temperatures and indentation loads, the critical load required for micro-fracture initiation was exceeded.