A method is provided for generating Acknowledgement/Negative Acknowledgement (ACK/NACK) information by a user equipment (UE) in a wireless communication system supporting carrier aggregation. The UE receives, from a base station (BS), a plurality of codewords through a plurality of downlink carriers. Each of the plurality of downlink carriers support one or more codewords according to a transmission mode. The transmission mode is independently configured per each of the plurality of downlink carriers. The UE determines a total number of ACK/NACK bits, and generates a sequence of the ACK/NACK bits according to the total number of the ACK/NACK bits. The UE determines the total number of ACK/NACK bits based on a total number of the plurality of downlink carriers and a type of each transmission mode independently configured per each of the plurality of downlink carriers.