Nanoporous crystals are widely studied and used for applications in H2 storage, CO2 capture, petrochemical catalysis and many other applications, yet the imaging of their atomic structure has proven difficult because of their radiation sensitivity and the small size of these microcrystals. This chapter describes the development of the new modes of electron microscopy needed to study them, and compares these with traditional methods such as x-ray diffraction. This class of materials has traditionally been dominated by the zeolites and zeotype materials, but has recently been expanded to include meso-/macroporous crystals and other new framework structures (MOFs, ZIFs COFs, etc.). Using different building blocks or units, versatile crystal structures have been synthesized for various applications. Their properties and functions are governed primarily by periodic arrangements of pores and/or cavities and their surroundings with various atomic moieties inside crystals. In this chapter, electron microscopy studies of nanoporous materials are discussed from different perspectives. Special attention is paid to the observation of fine defect structures, through careful analysis of electron diffraction, high-resolution images and spectroscopy data. The experimental conditions for imaging beam-sensitive materials, such as MOFs, are described. The contents have been divided into sections based on the types of materials and their geometric features. Examples of structure analysis of various nanoporous materials are given and discussed. New technical developments and existing challenges are described.