This paper addresses the problem of the simultaneous state and input estimation for hybrid systems when subject to input disturbances. The proposed algorithm is based on the moving horizon estimation (MHE) method and uses mixed logical dynamical (MLD) systems as equivalent representations of piecewise affine (PWA) systems. So far the MHE method has been successfully applied for the state estimation of linear, hybrid, and nonlinear systems. The proposed extension of the MHE algorithm enables the estimation of unknown inputs, or disturbances, acting on the hybrid system. The new algorithm is shown to improve the convergence characteristics of the MHE method by reducing the delay of convergent estimates, while assuring convergence for every possible sequence of input disturbances. To ensure convergence the system is required to be incrementally input observable, which is an extension to the classical incremental observability property. (c) 2006 Elsevier Ltd. All fights reserved.