An instrument tray assembly including a tray and an optional cover for the storage, transport and sterilization of medical instruments is disclosed. Each tray and cover is perforated to permit the flow of sterilizing medium therethrough, and each is comprised of materials which will withstand soaking and steam or gas autoclaving. Interchangeably disposed along the surfaces of the tray and cover are a plurality of support members, each including variously dimensioned notched receptacles for receiving medical instruments. Each tray may also include a set of handles which may be extended at a variety of angles, thereby avoiding contact and possible contamination between gloved hands and instruments, depending upon the orientation of each handle. Alternative embodiments for resilient instrument support members are disclosed. One embodiment includes resilient projections which are insertable directly into the perforations on the trays and covers. An alternative embodiment further includes a rigid extrusion. The extrusion is screwed to the surface of the tray or cover and the instruments are inserted into variously dimensioned receptacles on the support mounts. The trays may be used independently, interlockingly stacked one upon another, used in association with a locking cover, or covered then stacked together. The unique structure of the feet permits the trays to interlock in any of these combinations, to prohibit damage to the instruments contained therein. Optional locks which engage the cover further secure the instruments.