A method of performing hybrid automatic repeat request (HARQ) in a carrier aggregation system is provided. The method includes: monitoring a downlink (DL) grant for initial DL data transmission in a first DL component carrier (CC); receiving initial DL data through a second DL CC indicated by the DL grant; decoding the initial DL data; transmitting a not-acknowledgment (NACK) signal when decoding of the initial DL data fails; monitoring a DL grant for retransmission of the DL data in the first DL CC; and receiving DL data retransmitted through the second DL CC, wherein the second DL CC is any one of a plurality of DL CCs having a predetermined link relation with the first DL CC, and the DL grant for the initial transmission includes a carrier indication field indicating the second DL CC and resource allocation information for the initially transmitted DL data.