A surgical instrument tray shipping tote identification system is provided. During transit to or from a medical facility, processing center, distribution center or other location, multiple surgical instruments trays are placed in an instrument tray shipping tote. Each instrument tray includes at least one RFID transponder tag storing identification information about that tray. The shipping tote has a bar coded shipping label affixed to one surface generated at the point of origin. When the tote arrives at the distribution center, it is placed on a conveyor system that includes a reading station having an RFID transceiver and a bar code reader. Information read from the RFID transponder tags and the bar code label is transmitted by a controller to an external database to check for any off-nominal status indicators. Once this check is performed, an indication is sent back to the controller and an appropriate indicator on the identification system is activated.