A method and apparatus for transmitting a pilot in a wireless communication system is provided. A pilot generating unit generates the pilot. A transmission circuitry transmits the pilot and a radio signal. A a processor assigns a first index and a second index to each of a plurality of pilot patterns, determines a selection pilot pattern having a first selection index and a second selection index calculated based on a cell ID, which are respectively identical with the first index and the second index, from among the plurality of pilot patterns, and maps the generated pilot to a resource element based on the selection pilot pattern.