Perfluorooctane sulfonate (PFOS) is a typical perfluorinated compound and a new environmental chemical pollutant found worldwide. PFOS is a potential threat to the environment and public health. Studies on PFOS pollution in China have focused on the aquatic environment and some aquatic marine organisms, but little attention has been given to wild populations of freshwater fish. The upper Yangtze River is inhabited by 112 endemic and several rare fish species. However, the effect of PFOS pollution on fish in this area remains unclear. Brass gudgeon (), the main commercial fish species in this area, was sampled at Baixi, Yibin, Luzhou, and Chongqing cities in April, September, and December 2013, respectively, to clarify the status of PFOS residues in fish inhabiting the upper Yangtze River. A total of 36 brass gudgeon individuals were sampled, and PFOS content in 98 tissue samples, including three different fish tissues, were detected by ultra-performance liquid chromatography-tandem mass spectrometry. A mean value of 2.72 ng/g PFOS (range, 0.33-10.14 ng/g) was detected in all fish samples. The highest mean PFOS concentration was found in liver (5.56 ng/g), followed by muscle (1.39 ng/g), and the lowest concentration was detected in gonad (0.62 ng/g). A highly significant difference in PFOS concentration was observed among different tissues ( < 0.01).These results are consistent with some previous studies on PFOS concentrations in wildlife; that is, PFOS concentrates more easily in the liver than other tissues, which may be explained by the high binding affinity of PFOS for liver fatty-acid proteins. In addition, muscle PFOS concentrations were significantly different among different river reaches (main effects ANOVA, < 0.05). The PFOS concentrations in all detected tissues increased significantly with increasing fish age (main effects ANOVA, ≤0.05), indicating that tissue PFOS concentrations may be related to food items or physiological parameters of different age groups of fish. The PFOS concentrations detected in brass gudgeon were lower compared with levels measured in species worldwide, indicating a relatively low level of PFOS pollution in fish species in the upper Yangtze River.