A method and apparatus for transmitting a downlink signal in a multiple input multiple output (MIMO) wireless communication system is disclosed. A method for receiving a downlink signal from a base station to a user equipment in a multiple input multiple output (MIMO) system, which supports dual layer transmission based on first and second antenna ports, comprises receiving downlink control information (DCI) through a downlink control channel; and receiving downlink data through a downlink data channel, the downlink data including one or more of a first transport block and a second transport block, wherein the downlink control information includes a new data indicator (NDI) for each of the first and second transport blocks, and if the first transport block is disabled and the second transport block is enabled, the new data indicator for the first transport block indicates an antenna port through which the second transport block is received.