The primary objective of Structural Control (SC), in the context of real-time control of Flexible Manufacturing Systems (FMS), is to ensure deadlock-free operation of these systems. However, from the performance perspective, the application of structural control poli-cies (SCP's) during the system operation should be viewed as an additional set of constrains to be considered during the evaluation of the effective capacity of the FMS. The work developed in this paper aims at the development of computational models able to provide good capacity esti¬mates of the structurally controlled FMS. Two approaches are discussed: The first approach is based on a Continuous-Time Markov Chain (CTMC) model, and leads to very accurate estimates of the system capacity, but due to its very high (nonpolynomial) computational complexity, it can only be applied to small-sized FMS. Its value basically lies in the fact that it can function as a pilot towards the development of other, more approximate, but computationally tractable techniques. Such a technique is developed in the second part of the paper. Both approaches are demonstrated and tested on a small example.