This paper documents the accumulation and emerging levels of Persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs) and polybrominated diphenyl ethers (PBDEs) found in the tissues of the migrating salmon species Oncorhynchus tshawytscha (Chinook salmon) in the Chilean Patagonia area. Even though salmon are not native to the southern hemisphere, reports indicate that Chinook salmon in the last few years have performed natural free-living style cycling, returning to rivers in the southern Patagonia area. Our study seeks to determine the presence and levels of PCB's and PBDE's in wild Chinook salmon in the northern part of the Chilean Patagonia, analyzing their relation with physiological parameters. Fish were sampled at the end of their entire life cycle when they returned to two principal rivers in the Aysen region in southern Chile. A number of fish (12) were sacrificed in situ and muscle samples were taken for PCBs measurements (sum 44 congeners) by gas chromatography electron capture detector (GC-ECD) and a number of PBDEs congeners, by gas chromatography mass spectrometry with negative chemical ionization detection (GC-MS NCI). Observed levels and patterns were characterized by concentrations of these POPs for PCBs ranging between 78 and 25.5 ng g(-1) wet weight and for PBDEs ranging between 272 and 1046 pg g(-1) wet weight, respectively. These ranges are among same levels reported in this same species in the northern hemisphere.