Purpose - To examine how a very large order assembly system can be designed and commissioned to achieve a throughput of filling 2,400 order totes/h with medical prescription orders. Design/methodology/approach - To combine RFID and bar code scanning, individual pill bottle handling, pill dispensing, pre-packaged carton dispensing with some computer directed manual operations were key to meeting a goal of automatically filling tens of thousands of line items per day. Findings - Combining automated pill dispensing with automated small item order filling and computer directed pick-to-light manual item picking results in a single integrated system. A careful design by experienced suppliers is important to achieving successful commissioning in a timely manner. Read/write RFID technology plays an important role in insuring accuracy and traceability of each prescription bottle. Originality/value - Shows that complex order filling applications such as the highly regulated medical prescription filling can be automated to obtain improvements in accuracy and through put while reducing direct labor costs.