Molecular simulations were performed to determine the structure and behavior of methane and H2O in the interlayer of various montmorillonite clays. Molecular dynamics using NPT ensembles and large simulation supercells-comprised of Na-, K-, Ca-, and Mg-montmorillonite with methane and H2O-provide all-atom trajectories for simulation times up to 200 ps. Simulated X-ray diffraction patterns for the equilibrated structures exhibit basal (001) d-values that range from 23 Angstrom to 24 Angstrom. Radial distribution functions for carbon-carbon, oxygen-oxygen, and carbon-oxygen derived from the trajectories indicate an interlayer structure that is different from the bulk methane hydrate and from methane in aqueous solution. Some order of the methane hydrate structure is preserved within the interlayer and is related to the formation of methane clathrate structures with H2O and the clay surfaces and the formation of a hydrogen-bonded network in the interlayer. The theoretical results support the recent experimental observation of a stable methane hydrate intercalate with Na-montmorillonite.