Nowadays, small and medium-sized earthquakes occur frequently in the west coast of Korea. The earthquake induced damages on the harbor structure such as quay wall possibly make a severe impact on national economy. Therefore, not only a seismic design for the structures but warning system for seismic damage right after the occurrence of earthquake should be developed. In this study, seismic fragility analysis was performed to be given to earthquake damage prediction system for quay wall structures in Busan and Incheon harbor. Four types of structures such as pier-type, caisson type, counterfort type, block-type were analyzed and fragility curves of functional performance level and collapse prevention level based on displacement criteria were found. Regression analyses by using the results of the two ports were done for possible use in other port structures.