During the past decade, MIMO techniques have experienced a great interest in wireless communication systems. Also Cognitive Radio has been recognized as an advanced mean to effectively enhance the spectrum utilization. This paper investigates the comparison between precoding and prewhitening schemes for MIMO cognitive radio system where the primary and secondary systems sharing the channel side information. In the precoding scheme, the capacity of the system is maximized with reduced interference power. This is achieved by sending the information through the channel which is having the minimum singular value of the interference channel. In prewhitening scheme discussed, based on the Channel State Information, precoding matrix was decomposed in to direction and magnitude components. The interference can be minimized by using only the direction information of the interference channel. The performances of both the schemes have been analyzed and discussed. From the simulation results it is observed that both schemes are providing improved capacity with the minimum interference power.