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We propose a blind identification method for multiple-input multiple-output (MIMO) single-carrier zero-padding block-transmission systems. The method uses periodic precoding on the source signal before transmission. The estimation of the channel impulse response matrix consists of two steps: 1) obtain the channel product matrix by solving a lower-triangular linear system; 2) obtain the channel impulse response matrix by computing the positive eigenvalues and eigenvectors of a Hermitian matrix formed from the channel product matrix. The method is applicable to MIMO channels with more transmitters or more receivers. A sufficient condition for identifiability is simply that the channel impulse response matrix is full column rank. The design of the precoding sequence which minimizes the noise effect in covariance matrix estimation is proposed and the effect of the optimal precoding sequence on channel equalization is discussed. Simulations are used to demonstrate the performance of the method.