Modeling layered intercalation compounds from first principles poses a problem, as many of their properties are determined by a subtle balance between van der Waals interactions and chemical or Madelung terms, and a good description of van der Waals interactions is often lacking. Using van der Waals density functionals we study the structures, phonons and energetics of the archetype layered intercalation compound Li-graphite. Intercalation of Li in graphite leads to stable systems with calculated intercalation energies of −0.2 to −0.3 eV/Li atom, (referred to bulk graphite and Li metal). The fully loaded stage 1 and stage 2 compounds LiC 6 and Li 1/2 C 6 are stable, corresponding to two-dimensional √ 3× √ 3 lattices of Li atoms intercalated between two graphene planes. Stage N > 2 structures are unstable compared to dilute stage 2 compounds with the same concentration. At elevated temperatures dilute stage 2 compounds easily become disordered, but the structure of Li 3/16 C 6 is relatively stable, corresponding to a √ 7× √ 7 in-plane packing of Li atoms. First-principles calculations, along with a Bethe-Peierls model of finite temperature effects, allow for a microscopic description of the observed voltage profiles.