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This paper deals with the diagnosis of discrete-time singularly perturbed systems presenting two time scales property. Parity space method is considered to generate the fault detection residual. The focus is in two directions. First, we discuss the residual illconditioning caused by the singular perturbation parameter. Then, the use of the slow subsystem is considered to make the fault diagnosis easier. It is shown that the designed diagnostic algorithm based on reduced order model is close to the one synthesized using the full order system. The developed approach aims at reducing the computational load and the ill-conditioning for stiff residual generation problem. Two examples of application are used to demonstrate the efficiency of the proposed method.