Porous and confined materials with periodic micro and mesoscale pores have attracted much attention, both from fundamental and, applied scientists. Increasingly, we are encountering new, structurally complex materials, whose structures cannot be solved/characterized by the usual methods available. Knowledge of their structures is essential for thorough understanding of their properties and further development. Therefore, the development of methods appropriate for structural analysis of these materials is a matter of urgency. Electron microscopy may be the best technique for this purpose, as long as we are interested in both local structures and average periodic structures. Here we describe general aspects of the structural analysis of periodic nanoporous materials and our latest achievements in this field.