The electrochemical and structural responses of silicon nanowires deposited by chemical vapor deposition are investigated. Transmission electron microscopy and X-ray diffraction experiments show the electrochemical lithiation of SiNWs is not a quantitative process in good agreement with cycling experiments performed as a function of cycling limits. The SiNWs are not deeply lithiated as revealed by TEM micrographs. Our results suggest the existence of two well-defined lithiation steps, first at ∼0.2 V into amorphous silicon and then into crystalline silicon at ∼0.1 V. Cycling SiNWs above 100 mV avoid the lithiation of c-Si which preserves the silicon 3-D architecture and results in good cycling performances. A stable capacity value of ∼500 mAh g−1 is achieved over at least 50 cycles.