An animal isolation and caging system which maximizes cage density within a ventilated rack is provided. The rack includes at least one air exhaust plenum, and at least one canopy disposed within the rack for ventilation of the cages housed in a rack system. The rack is capable of supporting a first cage within the rack below a first canopy, and also positioning a second cage below a second canopy. The filter top of the first cage provided by the invention also provides a filter retainer having a filter top retainer wall designed to be in contact with a first canopy unit forming an enclosed space so configured as to create an enclosed space from which the animal isolation and caging system of the invention creates a zone of negative pressure so as to permit air to be drawn into an air exhaust plenum or duct from the interior of the first cage through the top of the first cage.