A pharmacy prescription order identification system is disclosed that permits individual detection and tracking of prescription orders even when they are all contained within a bulk container. Each prescription order in the bulk container has a uniquely identified tag. The tag is uniquely coded such that a tag reader can substantially simultaneously read a plurality of tags, thereby facilitating bulk processing and tracking of prescription orders. In a preferred embodiment the computer system compares the detected prescription orders in a bulk shipment with a provided manifest and alerts a worker of any discrepancies found. The tag reader is preferably a hand-held wand.