Electron tomography (ET) is a useful tool to investigate three-dimensional details based on virtual slices of relative thick specimen, and it requires complicated procedures consisted of image acquisition steps and image processing steps with computer program. Although the complicated step, this technique allows us to overcome some limitations of conventional transmission electron microscopy: (1) overlapping of information in the ultrathin section covering from 30 nm to 90 nm when we observe very small structures, (2) fragmentation of the information when we study larger structures over 100 nm. There are remarkable biological findings with ET, especially in the field of neuroscience, although it is not popular yet. Understanding of behavior of synaptic vesicle, active zone, pooling and fusion in the presynaptic terminal have been enhanced thanks to ET. Some sophisticated models of postsynaptic density with ET and immune labeling are introduced recently. In this review, we introduce principles, practical steps of ET and some recent researches in synapse biology.