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Performance of high speed communication systems is negatively affected by oscillator phase noise (PN). In this paper joint estimation of channel gains and Wiener PN in multi-input multi-output (MIMO) systems is analyzed. The signal model for the estimation problem is outlined in detail. In order to reduce overhead, a low complexity data-aided least-squares (LS) estimator for jointly obtaining the channel gains and PN parameters is derived. In order to track PN processes over a frame, a new decision-directed extended Kalman filter (EKF) is proposed. Numerical results show that the proposed LS and EKF based PN estimator performances are close to the CRLB and simulation results indicate that by employing the proposed estimators the bit-error rate (BER) performance of a MIMO system can be significantly improved in the presence of PN.