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A two-stage antenna subset selection scheme is proposed to maximize the channel capacity of amplify-and-forward multiple-input multiple-output relay systems. To reduce the computational complexity of the antenna selection process, the receive and transmit antenna selections are separated in a two-stage algorithm. In stage 1, a subset of receive antennas is selected at the relay node. A subset of transmit antennas is then selected at the relay node in stage 2. The simulation results demonstrate that the proposed scheme achieves nearly the same channel capacity with a reduced amount of computational complexity as compared to an exhaustive search.