In this paper, we propose an integrated methodology for the reliability and performance analysis of fault-tolerant systems. This methodology uses a behavioral model of the system dynamics, similar to the ones used by control engineers when designing the control system, but incorporates additional artifacts to model the failure behavior of the system components. These artifacts include component failure modes (and associated failure rates) and how those failure modes affect the dynamic behavior of the component. The methodology bases the system evaluation on the analysis of the dynamics of the different configurations the system can reach after component failures occur. For each of the possible system configurations, a performance evaluation of its dynamic carried out to check whether its properties, e.g., accuracy, overshoot, or settling time, which are called performance metrics, meet system requirements. After all system configurations have been evaluated, the values of the performance metrics for each configuration and the probabilities of going from the nominal configuration (no component failures) to any other configuration are merged into a set of probabilistic measures of performance. To illustrate the methodology, and to introduce a tool that we developed in MATLAB/SIMULINK (R) that supports this methodology, we present a case-study of a lateral-directional flight control system for a fighter aircraft.