A method and apparatus for transmitting a pilot signal in a wireless communication system. A reference cell scrambling code or one of a plurality of additional cell scrambling codes is selected for each combination of one of a plurality of first scrambling codes (PSCs) applied to a first synchronization channel (P-SCH) and one of a plurality of second scrambling codes (SSCs) applied to a second synchronization channel (S-SCH). It is determined whether to transmit the pilot signal using the reference cell scrambling code or one of the plurality of additional cell scrambling codes. The reference cell scrambling code or the additional cell scrambling code is generated according to the determination. The pilot signal is transmitted using the generated reference cell scrambling code or the additional cell scrambling code.