Individual whole body homogenates of 4 year old lake trout (Salvelinus namaycush) samples collected in 2001 from each of the Great Lakes were extracted using a novel fluorophilicity cleanup step and analyzed for perfluoroalkyl compounds (PFCs). Standard addition and internal standardization were used for quantification. Results were reported (+/- SE) for perfluorinated carboxylates (PFCAs), perfluorinated sulfonates (PFSAs), and unsaturated fluorotelomer carboxylates (8:2 and 10:2 FTUCA). The lowest average concentration of sigmaPFC was found in samples from Lake Superior (13+/-1 ng g(-1)), while the highest average concentration was found in samples from Lake Erie (152+/-14 ng g(-1)). Samples from Lake Ontario (60+/-5 ng g(-1)) and Lake Huron (58 +/-10 ng g(-1)) showed similar average sigmaPFC concentrations, although the perfluorinated sulfonate/carboxylate ratios were different. The major perfluoroalkyl contaminant observed was perfluorooctane sulfonate (PFOS) with the highest concentration found in samples from Lake Erie (121+/-14 ng g(-1)), followed by samples from Lake Ontario (46+/-5 ng g(-1)), Lake Huron (39 +/-10 ng g(-1)), Lake Michigan (16+/-3 ng g(-1)), and Lake Superior (5+/-1 ng g(-1)). Perfluorodecane sulfonate (PFDS) was detected in 89% of the samples, with the highest concentration in Lake Erie samples (9.8+/-1.6 ng g(-1)), and lowest concentration in samples from Lake Superior (0.7 +/- 0.1 ng g(-1)). Statistically significant correlations were observed between PFOS and PFDS concentrations, and PFOS concentration and body weight, respectively. The PFCAs were detected in all samples, with the highest total average concentration in samples from Lake Erie (19 ng g(-1)), followed by samples from Lake Huron (16 ng g(-1)), Lake Ontario (10 ng g(-1)), Lake Michigan (9 ng g(-1)) and Lake Superior (7 ng g(-1)). The compounds with significant contributions to the sigmaPFCA concentrations were PFOA and C9-C13-PFCAs. The 8:2 FTUCA was detected at concentrations ranging between 0.1 and 0.2 ng g-1, with the highest level in samples showing also elevated concentrations of PFOA (4.4 ng g(-1) for Lake Michigan vs 1.5 ng g(-1) for all other samples). The 10:2 FTUCA was detected only in 9% of all samples (nd, 45 pg g(-1)). For those PFCs where we determined lake water concentrations, the highest log BAFs were calculated for PFOS (4.1), PFDA (3.9), and PFOSA (3.8).