The present market conditions require manufacturing systems to expand their actions under the dynamic and uncertain production environment. To deal with such conditions, new technologies support increased manufacturing flexibility and automation. Machine and routing flexibility are the most common flexibility types employed in manufacturing systems. This paper presents a framework based on Taguchi experimental design for evaluating the effects of varying levels of machine and routing flexibility on the performance of an FMS. The system performance measures considered are makespan, average waiting time (AWT), and average utilisation (AUR). Other factors that will affect the system performance are also investigated, such as number of parts and control rules. Results of simulation study indicate that number of parts and routing flexibility are the two most important factors influencing the FMS performance; however, there are some optimal combinations of factors that represent the best system performance under the given set of operating conditions.