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Perfluoroalkyl acids (PFAAs) are ubiquitous in the environment. They are prone to accumulate in organisms and have raised public attention in recent decades. Feather samples have been successfully applied as nondestructive indicators for several contaminants. However, a sophisticated analytical method for determining PFAAs in feathers is still lacking. In the present study, a series of conditions, such as the use of the solid-phase extraction cartridge type and extraction/digestion methods, were optimized for the analysis of 13 PFAAs in feathers. According to the spiked recoveries, a weak-anion exchange cartridge was chosen and the methanol was selected as the extraction solvent. In the present study, an optimized pretreatment procedure combined with high-performance liquid chromatography-electrospray ionization-tandem mass spectrometric (HPLC-ESI-MS/MS) method was established for the determination of PFAAs in feathers. The recoveries and method detection limits of the PFAAs ranged from 71 to 120% and 0.16 to 0.54 ng/g, respectively. Finally, 13 PFAAs in four accipiter feather samples from Nam Co Basin, Tibetan Plateau, were analyzed, indicating that PFOS was the predominant PFAA in accipiter feathers, with an average of 4.67 ng/g, followed by the short-chain PFAAs, PFBS and PFBA, with averages of 1.91 and 1.39 ng/g, respectively. These results partly indicated the current situation of PFAA pollution in the Nam Co Basin, especially the existence of short-chain PFAAs in this region.