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In multiple input multiple output (MIMO) orthogonal frequency division multiplexing (OFDM) systems, some subcarriers are often retained as virtual subcarriers for easier filter implementation. In this case, the performance of Discrete Fourier Transform (DFT)-based channel estimation will be degraded significantly due to dispersive distortion of actual channel impulse response (CIR). To deal with this problem, we analyze the effect of virtual subcarriers on channel estimation in theory and propose an effective channel estimation scheme in the present paper. The proposed method, which is based on Schur recursive algorithm, can expand channel frequency response (CFR) into all subcarriers with quite concise operations. Finally, simulation results show that the proposed scheme outperforms LS estimator and DFT-based channel estimator, in terms of both MSE and FER.