Separation technology is central to industries as diverse as petroleum, pharmaceuticals, mining and life sciences. Metal–organic cages, a class of molecular containers formed via coordination-driven self-assembly, show great promise as separation agents. Precise control of the shape, size and functionalization of cage cavities enables them to selectively bind and distinguish a wide scope of physicochemically similar substances in solution. Extensive research has, thus, been performed involving separations of high-value targets using coordination cages, ranging from gases and liquids to compounds dissolved in solution. Enantiopure capsules also show great potential for the separation of chiral molecules. The use of crystalline cages as absorbents, or the incorporation of cages into polymer membranes, could increase the selectivity and efficiency of separation processes. This Review covers recent progress in using metal–organic cages to achieve separations, with discussion of the many methods of using them in this context. Challenges and potential future developments are also discussed.