The microstructure of epitaxial CuInS2, CuGaSe2 and polycrystalline CuInS2 films was studied by transmission electron microscopy. We found that the vapour-phase epitaxy of CuInS2 below the transition temperature T-c results in films with chalcopyrite and CuAu-like structures.. The formation of CuAu-like ordered phases within the films is independent of the substrate orientation, whereas the amount of CuAu-like ordered Cu and In atoms can be influenced by the substrate orientation. Thr co-existence of chalcopyrite and CuAu-like ordering of the metal atoms was also found in polycrystalline CuInS2 films prepared by sulphurization of Cu/In metal precursor at a temperature below T-c. In contrast, vapour-phase epitaxy of CuGaSe2 below T-c provides only films with the chalcopyrite structure. The experimental finding is in good agreement with the results of first-principle band-structure calculations.