In this paper, a contribution to modeling and fault diagnosis of rotor and stator faults of a Self-Excited Induction Generator (SEIG) in an Isolated Wind Energy Conversion System (IWECS) is proposed. In order to control the speed of the wind turbine, while basing on the linear model of wind turbine system about a specified operating point, a new Fractional-Order Controller (FOC) with a simple and practical design method is proposed. The FOC ensures the stability of the nonlinear system in both healthy and faulty conditions. Furthermore, in order to detect the stator and rotor faults in the squirrel-cage self-excited induction generator, an on-line fault diagnostic technique based on the spectral analysis of stator currents of the squirrel-cage SEIG by a Fast Fourier Transform (FFT) algorithm is used. Additionally, a generalized model of the squirrel-cage SEIG is developed to simulate both the rotor and stator faults taking iron loss, main flux and cross flux saturation into account. The efficiencies of generalized model, control strategy and diagnostic procedure are illustrated with simulation results. (C) 2014 Elsevier Ltd. All rights reserved.