We report observations of microstructural changes in {100} and {110} oriented silicon wafers during initial lithiation under relatively high current densities. Evolution of the microstructure during lithiation was found to depend on the crystallographic orientation of the silicon wafers. In {110} silicon wafers, the phase boundary between silicon and Li x Si remained flat and parallel to the surface. In contrast, lithiation of the {100} oriented substrate resulted in a complex vein-like microstructure of LixSi in a crystalline silicon matrix. A simple calculation demonstrates that the formation of such structures is energetically unfavorable in the absence of defects due to the large hydrostatic stresses that develop. However, TEM observations revealed micro-cracks in the {100} silicon wafer, which can create fast diffusion paths for lithium and contribute to the formation of a complex vein-like Li x Si network. This defect-induced microstructure can significantly affect the subsequent delithiation and following cycles, resulting in degradation of the electrode.