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This paper proposes a practical multi-input multi-output (MIMO) closed loop parameters identification procedure for robot manipulators. It is based on the weighted least squares (WLS) method, coupled with particular solutions to facilitate the estimation, reducing the noise effect. More precisely, a two steps procedure to reduce the condition number of the input data matrix with optimal trajectory planning, and a method to estimate the variances matrix to be used as a weight matrix for the WLS method are illustrated. Moreover, the identification problem is solved with reference to an MIMO coupled system. A closed loop identification is needed because the system is open loop unstable, and because the robot has to track an optimal reference input so as to correctly execute the identification procedure. Some solutions are also presented to overtake common identification problems, such as the bias of the estimated parameters, the presence of outliers, the necessity of balancing the kinematics of the third link, and the reduction of the sensitivity to noise of the estimate. The presented procedure has been successfully experimentally tested on a COMAU SMART3-S2 industrial manipulator used in a planar configuration.