Provided are a method and apparatus for transmitting a reference signal in a multi-antenna system. A terminal generates a plurality of reference signal sequences in which cyclic shift values different from each other are allocated to the respective plurality of layers, and generates a single carrier-frequency division multiple access (SC-FDMA) symbol to which the plurality of reference signal sequences are mapped. The SC-FDMA symbol is transmitted to a base station via a plurality of antennas. The cyclic shift values allocated to the respective layers are determined on the basis of a first cyclic shift value, which is a cyclic shift value allocated to a first layer from among the plurality of layers, and cyclic shift offsets which are allocated to the respective layers and which are different from each other.