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In this paper, a generalized subspace-based channel estimation algorithm is proposed for the multiple-input multiple-output orthogonal-frequency-division-multiplexing (MIMO-OFDM) systems in doubly-selective channels. To handle the rapid variation of fading within a transmission block, the subspace projection method is employed to approximate the channels, based on which a linear minimum mean square error (LMMSE) estimator is derived. Moreover, the mean square error (MSE) and corresponding Cramer-Rao Bound (CRB) of the proposed estimator are theoretically derived. By the aid of Monte Carlo simulation, the theoretical analysis is validated, and the bit error ratio (BER) performance is obtained.