The need for a new Quality Control approach has risen recently especially when dealing with automated systems in industry. The high cost of automated manufacturing systems requires a good quality control system that would improve production, reduce the number of scrapped products and help fast decision making when deviations from accepted quality levels occur. The situation becomes more complicated when dealing with Flexible Manufacturing Systems (FMS). Those systems are known for their capability to produce different types of products in moderate quantities. This in its turn requires an effective and flexible quality control system. This research studies the development of an Expert Quality Control System (EQCS) that is based on the available computer technology in flexible manufacturing. The purpose of EQCS is to help quality engineers diagnose deviations from required quality requirements, and to take the right decisions to improve the process and yield product quality.