Local structure and site distribution of extra-framework copper ions in over-exchanged Cu-MCM22 zeolite were determined by a combination of high resolution X-ray powder diffraction and computational analysis. X-ray diffraction data suggested the presence of three Cu sites in six-membered rings and one site in a five-membered ring close to the interlamellar region, inside the MCM-22 supercage, whereas no Cu ions were found within the sinusoidal channels. First principle molecular orbital DFT calculations were employed to obtain, for the first time, an accurate structural description of the Cu(I) sites in the supercage, adding a structural and energetic interpretation to previous IR and EPR studies. The combined experimental and computational study suggested that Cu(I) sites facing 6-MRs are particularly stable. In general 5- or 4-fold coordination sites are located in 6-MRs while 2- or 3-fold coordination sites are located in 5-MRs. Three preferentially occupied sites were found in copper-exchanged MCM-22. X-ray photoelectron spectroscopy suggested the formation of dispersed Cu close to the surface of MCM-22 crystallites, easily reduced to Cu(I) under ultrahigh vacuum conditions.