This paper discusses a joint adaptive channel estimation and transceiver design scheme for MIMO two-way relay systems. In order to reduce the computational complexity at the transmitting nodes, the transceiver is implemented at the relay station. Adaptive transceiver consists of an adaptive postequalizer known as receive filter and an adaptive pre-equalizer known as transmit filter. The design of adaptive pre-equalizer requires the knowledge of Channel State Information (CSI) between nodes and relay station. So a channel tracking adaptive filter should be implemented at the relay. Due to the structure of a two-way relay system, the training signals used to train the receive filter can be used to train the channel tracking filter. Thus the adaptive channel estimator and receive filter work simultaneously. The channel estimate is then used to design the transmit filter. The adaptive filters are implemented using the NLMS algorithm. The performance of the proposed scheme is verified by making use of MATLAB simulations. © 2013 IEEE.