A method of transmitting a midamble for channel estimation of multiple antennas performed by a base station in a system having segregated uplink and downlink frequency bands is provided. The method includes transmitting midamble information indicating presence of the midamble within a downlink frame to a user equipment (UE), and transmitting the midamble on a single downlink subframe among at least one downlink subframe included in the downlink frame or on a common zone to the UE by using the multiple antennas. A scheduling overhead of a base station and other overheads can be reduced by decreasing the number of transmissions of a midamble on one downlink frame, and thus limited radio resources can be effectively used.