Perfluorinated compounds (PFCs) have a wide range of domestic and industrial applications, but they are persistent in the environment. Perfluorooctanoic acid (PFOA) and perfluorooctanesulfonate (PFOS) are among the metabolites of PFCs and occur at high concentration in the environment. Korea is the largest importer of PFC compounds in the world, therefore, the accumulation of these compounds is possible. In this study, the concentrations of PFOS and PFOA were determined in water samples taken from sewage treatment plants (STPs) and the Han River in Seoul, Korea. After extraction with a HLB cartridge, PFCs in the samples were analyzed by HPLC with an ion trap mass spectrometry in electrospray negative mode. Limits of detection was between 1 and 1.6 ng/l. The result showed that the concentrations of PFOS and PFOA in effluent and influent of the four STPs in Seoul were 60~570 ng/l, and not detected (nd)~254 ng/l, respectively. The levels of PFOS and PFOA were higher in the effluents which passed through the treatment process than in influent water samples which was against expectation. The concentration of PFOA and PFOS in the Han River was 60~570 ng/l and nd~254 ng/l, respectively. PFOA was detected in every sample, but PFOS was only detected in the downstreams of the Han River. This result indicates that there is comprehensive contamination of PFCs in the aquatic environment in Korea.