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Oscillator phase noise limits the performance of high speed communication systems since it results in time varying channels and rotation of the signal constellation from symbol to symbol. In this paper, joint estimation of channel gains and Wiener phase noise in multi-input multi-output (MIMO) systems is analyzed. The signal model for the estimation problem is outlined in detail and new expressions for the Cramér-Rao lower bounds (CRLBs) for the multi-parameter estimation problem are derived. A data-aided least-squares (LS) estimator for jointly obtaining the channel gains and phase noise parameters is derived. Next, a decision-directed weighted least-squares (WLS) estimator is proposed, where pilots and estimated data symbols are employed to track the time-varying phase noise parameters over a frame. In order to reduce the overhead and delay associated with the estimation process, a new decision-directed extended Kalman filter (EKF) is proposed for tracking the MIMO phase noise throughout a frame. Numerical results show that the proposed LS, WLS, and EKF estimators' performances are close to the CRLB. Finally, simulation results demonstrate that by employing the proposed channel and time-varying phase noise estimators the bit-error rate performance of a MIMO system can be significantly improved.