Fault tolerant control can accommodate the component faults in a control system such as sensors, actuators, plants, etc. This dissertation presents two fault tolerant control schemes to accommodate the failures of power amplifiers and sensors in a magnetic suspension system. The homopolar magnetic bearings are biased by permanent magnets to reduce the energy consumption. One control scheme is to adjust system parameters by swapping current distribution matrices for magnetic bearings and weighting gain matrices for sensor arrays, but maintain the MIMO-based control law invariant before and after the faults. Current distribution matrices are evaluated based on the set of poles (power amplifier plus coil) that have failed and the requirements for uncoupled force/voltage control, linearity, and specified force/voltage gains to be unaffected by the failure. Weighting gain matrices are evaluated based on the set of sensors that have failed and the requirements for uncoupling x1 and x2 sensing, runout reduction, and voltage/displacement gains to be unaffected by the failure. The other control scheme is to adjust the feedback gains on-line or off-line, but the current distribution matrices are invariant before and after the faults. Simulation results have demonstrated the fault tolerant operation by these two control schemes.