Electron microscopic investigations of zeolites are reviewed. Scanning electron microscopy can show the appearance of zeolite crystals, e.g. their sizes and morphologies, and can also be used to look into the cores of crystals, revealing any abnormal microstructures, which often help us to elucidate actual crystal growth mechanisms. High resolution transmission electron microscopy is a powerful tool to directly image many pore systems and local defects in zeolites. The more advanced techniques, including spherical aberration corrected scanning transmission electron microscopy, high angle annular dark field imaging, high resolution energy dispersive X-ray spectroscopy, 3D electron tomography, etc., allow us to reveal much more structural details of zeolites and other porous materials such as metal–organic frameworks.