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In this paper, the detection and isolation of actuator faults (both measured and commanded) occurring in the engine breathing and the fueling systems of a spark-ignition direct-injection (SIDI) engine are described. The breathing system in an SIDI engine usually consists of a fresh air induction path via an electronically controlled throttle (ECT) and an exhaust gas recirculation (EGR) path via an EGR valve. They are dynamically coupled through the intake manifold to form a gas mixture, which eventually enters the engine cylinders for a subsequent combustion process. Meanwhile, the fueling system is equipped with a high-pressure common-rail injection for a precise control of the fuel quantity directly injected into the engine cylinders. Since the coupled system is highly nonlinear in nature, the fault diagnosis will be performed by generating residuals based on multiple nonlinear observers.