This work focuses on the design and control of intelligent Automatic Storage and Retrieval Systems (AS/RS) for Flexible Manufacturing Systems (FMS). The concepts are demonstrated, without loss of generality, on a laboratory prototype FMS involving a CNC lathe, a CNC milling machine, a robot and an AS/RS consisting of three rows and five columns. The design of the AS/RS is explained followed by its implementation and motion control being implemented on a low cost microcontroller. Further, an RFID-based system supports the identification of pallets, both empty and loaded with parts, hosted at specific cells of the AS/RS. Particular emphasis is given on the design of the user interface of the system, since the functions of the transport and handling may also be supplemented or even circumvented by the human. Optimization of the part storage assignment to AS/RS cells was achieved through a genetic algorithm minimizing total operating time and starting with a given production schedule that may or may not be optimal.