A methodology is presented for the design of integrated, model-based fault diagnosis and reconfigurable control systems for transport-reaction processes modeled by nonlinear parabolic partial differential equations (PDEs) with control constraints and actuator faults. The methodology brings together nonlinear feedback control, fault detection and isolation (FDI), and performance-based supervisory switching between multiple actuator configurations. Using an approximate, finite-dimensional model that captures the PDE's dominant dynamic modes, a stabilizing nonlinear feedback controller is initially designed for each actuator configuration, and its stability region is explicitly characterized in terms of the control constraints and actuator locations. To facilitate the fault diagnosis task, the locations of the control actuators are chosen in a way that ensures that the evolution of each dominant mode, in appropriately chosen coordinates, is excited by only one actuator. Then, a set of dedicated FDI filters, each replicating the fault-free behavior of a given state of the approximate system, are constructed. The choice of actuator locations ensures that the residual of each filter is sensitive to faults in only one actuator and decoupled from the rest, thus, allowing complete fault isolation. Finally, a set of switching rules are derived to orchestrate switching from the faulty actuators to healthy fall-backs in a way that preserves closed-loop stability and minimizes the closed-loop performance deterioration resulting from actuator faults. Precise FDI thresholds and control reconfiguration criteria that account for model reduction errors are derived to prevent false alarms when the reduced order model-based fault-tolerant control structure is implemented on the process. A singular perturbation formulation is used to link these thresholds with the degree of separation between the slow and fast eigenvalues of the spatial differential operator. The developed methodology is successfully applied to the problem of constrained, actuator fault-tolerant stabilization of an unstable steady-state of a representative diffusion-reaction process. (c) 2007 American Institute of Chemical Engineers