The crystal structure and lithium intercalation properties of commercially available synthetic and natural graphites were investigated using x-ray diffraction and electrochemical voltage spectroscopy techniques. It has been found that most graphites are a mixture of hexagonal and rhombohedral phases. A specific x-ray refinement program has been developed to extract the structural parameters of each of the two phases, such as their relative concentrations, structural disorders, layer sizes, and interlayer spacing, etc. The rhombohedral phase content may exceed 30% in some graphites. It was also observed that as the particle size of the graphite is reduced, the rhombohedral content is increased. The Lithium intercalation reactions in various graphites were investigated by using electrochemical voltage spectroscopy and the correlation between lithium intercalation reversibility, phase content, and structural disorder of the graphites is discussed in detail. A modified correlation model is developed to facilitate the understanding of the relation between the structures of graphite and the lithium intercalation properties. It was found that the total reversible lithium capacity is related to both the hexagonal and rhombohedral phase contents, and that the lithium intercalation mechanism in the two structures are similar.