The present invention generally comprises a container storage system for efficiently storing large capacity and small capacity containers or FOUPs. In one embodiment, each storage location within the stocker comprises a pair of spaced apart supports. A large capacity container or a small capacity container may be seated in any storage location. The storage locations are arranged within the stocker to minimize the amount of empty space between the supports of a storage location and a container seated in an adjacent storage location. In one embodiment, the vertical pitch between supports of adjacent storage locations is less than the height of a large capacity FOUP container shell. Thus, when a FOUP is seated in a storage location, its container shell extends between the supports of the storage location located directly above.