An automated case unit storage system (100, 200, 300, 400) for handling case units that are adapted for being palletized for shipping to or from a storage facility, the automated case unit storage system comprising: a multilevel storage structure, each level of the multilevel storage structure comprising a transport area and a storage area, the storage area including an array of storage shelves adapted to hold case units thereon; at least one substantially continuous lift for transporting at least one uncontained case unit to and from a predetermined level of the multilevel storage structure; and at least one autonomous transport vehicle being assigned to each level of the multilevel storage structure, the at least one autonomous transport vehicle having a frame configured to traverse the transport area of the respective level for transporting the at least one uncontained case unit between the substantially continuous lift and a predetermined storage location of the storage shelves on the respective level, the at least one autonomous transport vehicle being configured to directly or indirectly transfer the at least one uncontained case unit to and from the at least one substantially continuous lift, wherein each level of the multilevel storage structure further comprises an interface device configured for transferring the at least one case unit between the substantially continuous lift and the at least one autonomous transport vehicle, the at least one autonomous transport vehicle comprising vehicle fingers configured to pass through the slatted transfer shelves for transferring the at least one case units to or from the interface device, characterized in that the automated case unit storage system comprises: a controller configured to create at least one alternate access path through the transport area and storage area to a predetermined one of the case units when a predetermined access path is unavailable, and wherein the substantially continuous lift comprises slatted transport shelves and the interface device comprises fingers configured to pass through the slatted transport shelves for transferring the at least one case units to or from the substantially continuous lift, wherein the fingers of the interface device form a slatted transfer shelf. a multilevel storage structure, each level of the multilevel storage structure comprising a transport area and a storage area, the storage area including an array of storage shelves adapted to hold case units thereon; at least one substantially continuous lift for transporting at least one uncontained case unit to and from a predetermined level of the multilevel storage structure; and at least one autonomous transport vehicle being assigned to each level of the multilevel storage structure, the at least one autonomous transport vehicle having a frame configured to traverse the transport area of the respective level for transporting the at least one uncontained case unit between the substantially continuous lift and a predetermined storage location of the storage shelves on the respective level, the at least one autonomous transport vehicle being configured to directly or indirectly transfer the at least one uncontained case unit to and from the at least one substantially continuous lift, wherein each level of the multilevel storage structure further comprises an interface device configured for transferring the at least one case unit between the substantially continuous lift and the at least one autonomous transport vehicle, the at least one autonomous transport vehicle comprising vehicle fingers configured to pass through the slatted transfer shelves for transferring the at least one case units to or from the interface device, characterized in that the automated case unit storage system comprises: a controller configured to create at least one alternate access path through the transport area and storage area to a predetermined one of the case units when a predetermined access path is unavailable, and wherein the substantially continuous lift comprises slatted transport shelves and the interface device comprises fingers configured to pass through the slatted transport shelves for transferring the at least one case units to or from the substantially continuous lift, wherein the fingers of the interface device form a slatted transfer shelf. a controller configured to create at least one alternate access path through the transport area and storage area to a predetermined one of the case units when a predetermined access path is unavailable, and wherein the substantially continuous lift comprises slatted transport shelves and the interface device comprises fingers configured to pass through the slatted transport shelves for transferring the at least one case units to or from the substantially continuous lift, wherein the fingers of the interface device form a slatted transfer shelf.