The effect of surface structural damage on graphitic anodes, commonly observed in tested Li-ion cells, was investigated. Similar surface structural disorder was artificially induced in Mag-10 synthetic graphite anodes using argon-ion sputtering. Raman microscopy, scanning electron microscopy, and Brunauer–Emmett–Teller measurements confirmed that Ar-ion sputtered Mag-10 electrodes display a similar degree of surface degradation as the anodes from tested Li-ion cells. Artificially modified Mag-10 anodes showed double the irreversible charge capacity during the first formation cycle compared to fresh unaltered anodes. Impedance spectroscopy and Fourier transform infrared spectroscopy on surface-modified graphite anodes indicated the formation of a thicker and slightly more resistive solid electrolyte interphase (SEI) layer. Gas chromatography/mass spectroscopy analysis of solvent extracts from the electrodes detected the presence of new compounds with Mw on the order of 1600gmol−1 for the surface-modified electrode with no evidence of elevated Mw species for the unmodified electrode. The structural disorder induced in the graphite during long-term cycling may be responsible for the slow and continuous SEI layer reformation, and consequently, the loss of reversible capacity due to the shift of lithium inventory in cycled Li-ion cells.