To facilitate high-throughput analysis suitable for large epidemiological studies we developed an automated column-switching ultra-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) method for determination of perfluorocarboxylic acids (PFCAs; C5, C6, C7, C8, C9, C10, C11, C12, and C13), perfluoroalkyl sulfonic acids (PFSAs; C4, C6, C8, and C10), perfluorooctane sulfonamide (PFOSA), and five groups of structural perfluorooctane sulfonic acid (PFOS) isomers in human serum or plasma. The analytical procedure involves rapid protein precipitation using 96-well plates followed by an automated sample clean-up using an on-line trap column removing many potentially interfering sample components while through the mobile phase gradient the target analytes are eluted onto the analytical column for further separation and subsequent mass detection. The method was linear (R(2)<0.995) at concentrations ranging from 0.01 to 60ngmL(-1) with method detection limits ranging between 0.01 and 0.17ngmL(-1) depending on the analyte. The developed method was precise, with repeatability (n=7) and reproducibility (n=103) coefficients of variation between 2% and 20% for most compounds including PFOS (2% and 8%) and its structural isomers (2-6% and 4-8%). The method was in conformity with a standard reference material. The column-switching HPLC-MS/MS method has been successfully applied for the determination of perfluoroalkyl substances including structural PFOS isomers in human plasma from an epidemiological study.