A method and apparatus for performing a transport network layer (TNL) address discovery procedure in a wireless communication system is provided. A first eNodeB (eNB) transmits at least one of a TNL address of the first eNB and a TNL address of an X2-gateway (GW), and a source eNB identifier (ID). The eNB may further transmit an indication of X2 setup which indicates whether a direct X2 interface between the first eNB and a second eNB or an indirect X2 interface going through the X2-GW is to be set up.