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This paper considers the problem of robust channel estimation for direct-sequence code-division multiple-access (DS-CDMA) systems with time-varying multipath fading channels. Due to the lack of accurate knowledge of model dynamics and statistics of system noises, a polynomial channel estimator is developed by virtue of the Krein space theory. The estimator is calculated by performing a J-spectral factorization. In this paper, under some conditions, we obtain a closed-form solution to this J-spectral factorization, which greatly reduces the computational load of the estimator design. The simulation results show that the proposed estimator provides a robust estimation performance against various types of noises and modeling errors.