Robust state estimation and fault diagnosis are challenging problems in the research into nonlinear systems. In this paper a sliding mode observer is proposed for a class of nonlinear systems with unknown inputs and faults. Model uncertainties, disturbances and faults are represented as structured unknown inputs. We analyzed the robustness of sliding model control system and put forward a fault diagnosis method using sliding mode observer for fault diagnosis of uncertain control system. Robustness to model uncertainties and disturbances can be guaranteed for the sliding mode observer by disturbance decoupling. The method can supply a stable estimation of the state response of uncertain control system under normal disturbance, and furthermore realize the diagnosis for fault disturbance. The results proved the feasibility of the method.