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This paper develops a joint fine timing synchronization and channel estimation scheme for multiple-input multiple-output (MIMO) systems based on a well-designed training sequence arrangement. The proposed approach generalizes a first channel tap selection scheme and presents a majority vote refinement (MVR) of the timing estimates for different transmit-receive links. The MVR fully exploits the features of the training sequence arrangement and the MIMO diversity to improve timing synchronization as well as channel estimation. In addition, an optimal threshold for the proposed first channel tap selection scheme is derived based on a Rayleigh channel assumption. The optimal solution clearly reveals how the threshold should react to the channel statistics, the signal-to-noise ratio, the number of active transmit-antennas, and other design parameters. Based on this, a practical suboptimal threshold that requires neither pre-simulation nor prior information on the channel statistics is then proposed. Also, the performance of the proposed approach is analyzed with respect to threshold selection and MVR, and the theoretical results agree well with the simulation results in several channel models.