SEM images of round-shaped natural graphite, currently widely used as the anode active material of Li-ion batteries, show that the surface mainly consists of the basal plane, which suggests that the Li insertion/extraction reaction rate is quite limited. In contrast to this suggestion, however, the anode of commercial Li-ion batteries is capable of high rate charging/discharging. In order to explain this inconsistency, we propose that there are nano-holes in the graphene layers of the graphite allowing Li to be very easily inserted and extracted via the holes. Prior to the measurements a quantum chemical investigation was performed on the energy required for Li to pass through the hole in a graphene layer (E act). The results showed that the E act value is too high when the size is smaller than pyrene, but is fairly low for holes of the size of coronene, implying that Li can pass through the basal plane layer if there is a hole larger than coronene. Characterization of the rounded graphite sample and flaky natural graphite was conducted by constant-current charge/discharge cycle tests, X-ray diffraction (XRD), Raman spectroscopy, scanning electron microscopy (SEM), and high-resolution transmission electron microscopy (HRTEM). XRD revealed no appreciable difference between the rounded graphite and flaky natural graphite, in agreement with Raman data. A detailed analysis of the HRTEM results revealed the presence of a number of variously sized circular images. We believe that these are holes in the graphene layer through which Li can pass. The mechanism of formation of the holes is discussed.