The lithium-ion battery anode performance of graphites with and without high amounts of rhombohedral phase in the structure has been investigated. A main outcome was that in addition to possible graphite bulk structure effects, there are also strong influences of the graphite surface and the graphite “sub-surface” (part of the graphite bulk at the border of the particle near the surface) on the solid electrolyte interphase (SEI) formation process and on the tendency to solvent co-intercalation into graphite. Using transmission electron microscopy with atomic resolution, we indeed could determine unique and also different surface and “sub-surface” morphologies for the two graphites. In case of the graphite without rhombohedral phase, unique convoluted graphene layers could be determined at the prismatic surfaces; in case of the graphite with a high rhombohedral phase content a strongly disordered, approximately 1nm thick “sub-surface” layer could be determined. The anode performance depends primarily on these surface and “sub-surface” graphite properties and the used electrolytes. The differences in the “sub-surface” layer structure have a most significant influence on the performance in an ethylene carbonate/dimethyl carbonate electrolyte. The differences in surface structure and morphology are considered to have the highest impact in a propylene carbonate/ethylene sulfite-based electrolyte. For ethylene carbonate/diethyl carbonate electrolyte, the performance differences are small so that no strong dependence on surface or “sub-surface” structures could be observed.