The porous structure and the periodic array of cavities in ordered mesoporous materials with large, three-dimensionally arranged and interconnected pores is thoroughly described by combining electron tomography, small-angle X-ray diffraction, and nitrogen sorption techniques. We used the ability of the electron tomography to provide local three-dimensional information of a nano-object and compared the results to those of the other characterization techniques which furnish global information. We showed thus that the face-centered cubic (fcc) structure usually assigned to the FDU-12 materials is in fact an intergrowth of cubic and hexagonal close-packing structures. This agrees with small-angle X-ray scattering (SAXS) modeling, but for the first time a direct visualization of these stacking faults was achieved. Three-dimensional transmission electron microscopy (3D-TEM) provides also a direct and unique evidence of peculiar stacking defects ("z-shifted [111] areas"), as well as an estimate of their density, which have never been reported elsewhere. In addition, interstitial cavities were also observed, revealing the complex defective structure of this material. A direct observation of the nature of the connecting pores was also achieved for the first time, with a resolution limit of 2 nm. Finally, the characteristics of the porous network evidenced by 3D-TEM are used to explain and validate the results obtained by nitrogen sorption experiments.