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In this paper, we consider a channel estimation scheme for a two-hop nonregenerative MIMO relay system without the direct link between source and destination. This scheme has two phases. In the first phase, the source does not transmit while the relay transmits and the destination receives. In the second phase, the source transmits, the relay amplifies and forwards, and the destination receives. At the destination, the data received in the first phase are used to estimate the relay-to-destination channel, and the data received in the second phase are used to estimate the source-to-relay channel. The linear minimum mean-square error estimation (LMMSE) is used for channel estimation, which allows the use of prior knowledge of channel correlations. For phase 1, an algorithm is developed to compute the optimal source pilot matrix for use at the relay. For phase 2, an algorithm is developed to compute the optimal source pilot matrix for use at the source and the optimal relay pilot matrix for use at the relay.