The effect of surface structural damage on graphitic anodes, commonly observed in tested Li-ion cells, was investigated. Similar surface structural disorder in graphite was artificially induced in Mag-10 synthetic graphite anodes using argon-ion sputtering. Raman microscopy, scanning electron microscopy (SEM) and Brunauer Emmett Teller (BET) measurements confirmed that Ar-ion sputtered Mag-10 electrodes display 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 un-altered anodes. Impedance spectroscopy and Fourier transform infrared (FTIR) spectroscopy on surface modified graphite anodes indicated the formation of a thicker and slightly more resistive SEI layer. The structural disorder induced in the graphite during long-term cycling maybe 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.