First-principles calculations were performed to determine equilibrium geometries, static equation of state parameters, the energetics and orientation of the guest molecule inside the 5 and 56 cages, and vibrational frequencies of methane clathrate hydrate. According to our results, the progressive inclusion of one molecule in each clathrate cavity is always a stabilizing process up to saturation. The released energy is very similar for both types of cages. In agreement with the experimental observation of roto-vibrational spectra in this hydrate, we calculate an energy barrier of less than 0.5 kcal/mol, indicating free rotation of methane inside the cages. The stabilizing effect of applied pressure leads to a red shift of the O–H stretching frequencies of the water molecules of around 80 cm in average at 1 GPa.