We propose a greedy minimum mean squared error (MMSE)-based antenna selection algorithm for amplify-and-forward (AF) multiple-input multiple-output (MIMO) relay systems. Assuming equal-power allocation across the multi-stream data, we derive a closed form expression for the mean squared error (MSE) resulted from adding each additional antenna pair. Based on this result, we iteratively select the antenna-pairs at the relay nodes to minimize the MSE. Simulation results show that our algorithm greatly outperforms the existing schemes.