In situ electrochemical lithiation and delithiation processes inside a nanobattery consisting of an individual amorphous Si nanorod and ionic liquid were explored. Direct formation of the crystalline Li(22)Si(5) phase due to the intercalation of Li ions was observed. In addition, the role of the electrolyte-nanorod interface was examined. It was observed that the lithiation of Si nanorods is dominated by surface diffusion. Upon the delithiation process, partial decomposition of Li(22)Si(5) particles was observed which can explain the irreversible capacity loss that is generally seen in Si anodes. This study shows that the radial straining due to lithiation does not cause cracking in nanorods as small in diameter as 26 nm, whereas cracks were observed during the lithiation of 55 nm Si nanorods.