A method was performed to enable a combined analysis for quantifying levels of perfluoroalkyl substances (PFAS) and bile acids in human plasma samples from Taiwan. Protein precipitation and phospholipid removal was performed using a 96-well plate and analysed with ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MSMS). The instrumental analysis was performed with a reverse-phased chromatography. The mass analysis was carried out using multiple reaction monitoring (MRM) mode. A matrix matched calibration curve using new-born bovine serum (NBS) was used for the analysis of the PFAS and an external one point calibration for the bile acids. The twenty plasma samples were collected after an over-night fast and consisted of seventeen samples from patients undergoing haemodialysis and three samples from healthy controls. The variation between the healthy controls and the patient samples is observed where a higher concentration of L-PFOS, PFOA, PFNA and PFHxS was found in the control samples. It is explained that haemodialysis can decrease the amount of PFOS. The lower concentrations found in the human plasma was of PFHpA. 18 of 30 bile acids were detected but eight of them were selected for quantitative analysis. The concentration of the bile acids varied less between the three control samples and the seventeen patient samples when compared to the PFAS. The highest median value was found for CDCA whilst GHCA had the lowest median value. Taken together, the combined analysis of bile acids and PFAS was accomplished along with the determination of their concentration in human plasma.