This paper presents framework for fault tolerant controllers (FTC) that includes input saturation. The controller architecture known from FTC is based on the Youla-Jabr-Bongiorno-Kucera (YJBK) parameterization is extended to handle input saturation. Applying this controller architecture in connection with faulty systems including input saturation gives an additional YJBK transfer function related to the input saturation. In the fault free case, this additional YJBK transfer function can be applied directly for optimizing the feedback loop around the input saturation. In the faulty case, the design problem is a mixed design problem involved both parametric faults and input saturation.