VESTA is a three‐dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3, implementing new features including drawing the external morphology of crystals; superimposing multiple structural models, volumetric data and crystal faces; calculation of electron and nuclear densities from structure parameters; calculation of Patterson functions from structure parameters or volumetric data; integration of electron and nuclear densities by Voronoi tessellation; visualization of isosurfaces with multiple levels; determination of the best plane for selected atoms; an extended bond‐search algorithm to enable more sophisticated searches in complex molecules and cage‐like structures; undo and redo in graphical user interface operations; and significant performance improvements in rendering isosurfaces and calculating slices.