Abstarct: Current modern societies extremely depend on new technology and industrial systems, in such systems fault and therefore physical and financial damage may happen. The actuators fault causes reduction of control systems efficiency and in some cases; it causes complete damage in systems. Sensors fault may conceal the process natural level and put system away from its scope. In some industrials, during system fault, it is compulsory to turn off the system in order to prevent from more damages, although such process may be destructive. So identifying and organizing of fault playing key role in current technology and evaluating the fault tolerant control systems is important. In these systems, fault detection and isolation and reconfigurable control are very important and in this thesis were discussed. In this thesis at first we was evaluated the summary of fault tolerant control systems and fault detection and isolation then a new method have been presenting for MIMO systems and baxsed on Eigenstructure assignment for state observer, by this method a complete parametric exxpression for the observer gains are established in terms of a set of parametric vectors and closed loop poles. Then considering the importance of fault detection and isolation in fault tolerant control systems, this subject was discussed and evaluated by utilizing of bank of observers and the subject of the actuator fault isolation after its detection was discussed. Fault isolation is harder than fault detection and in this subject the research is unimportant. In case of complete evaluation of fault estimation in system by adding one appropriate regulation in common controller, we can near system behavior to fault free system; this subject was evaluated in this thesis and a new method suggested for fault estimations in actuator and sensors. . The simulation results corroborate the effectiveness and simplicity of the proposed methods.