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In this paper, we propose a novel whitening-rotation (WR) based semi-blind (SB) scheme for frequency-selective channel estimation in multiple-input multiple-output (MIMO) multi-carrier (MC) CDMA systems. This scheme is based on a low complexity multi-path multi-carrier decorrelator (MMD) receiver structure developed for the MIMO MC-CDMA system. It is shown that the MMD based receiver naturally enables the formulation of the SB scheme by reducing the frequency-selective MIMO MC-CDMA channel to a flat fading channel matrix of appropriate dimension. Thus, it results in a significant reduction in the computational complexity usually associated with frequency-selective MIMO channel estimation. Further, we derive the Cramer-Rao bound (CRB) to characterize the mean squared error (MSE) performance of the proposed SB scheme. For performance comparison of the proposed SB estimator, we also derive the training estimate and the uncertainty based robust estimate of the frequency-selective MIMO MC-CDMA channel. Simulation results demonstrate that the proposed SB scheme achieves a significantly lower MSE of estimation compared to the competing training and robust estimation schemes.