► First comparison of UHPLC–MS/MS and capillary LC–MS for the analysis of PFCs in water. ► UHPLC–MS/MS provides the best linearity and sensitivity and shortest analysis time. ► Capillary LC–MS attains the best precision and comparable sensitivity. ► UHPLC–MS/MS and capillary LC–MS possess a short running time. ► Both methods were successfully applied to real samples obtaining comparable results. In this work, the performance of ultra-high-performance liquid chromatography–tandem mass spectrometry (UHPLC–MS/MS) and capillary liquid chromatography–mass spectrometry (CLC–MS) has been studied for the analysis of eighteen perfluorinated compounds in water samples. UHPLC–MS/MS and CLC–MS analysis were carried out using a Zorbax C-18 column (50mm×2.1mm, 1.8μm) and a Zorbax SB-C18 column (150mm×0.5mm, 3.5μm), respectively, in gradient elution mode with a mobile phase of ammonium formate and methanol. Both techniques were compared with conventional LC–MS/MS in terms of speed, sensitivity, selectivity and resolution. Water samples were extracted by solid phase extraction (SPE). Mean absolute recoveries at two concentration levels, 6 and 60ngL−1, calculated from the eighteen compounds were: 77±12(s) and 82±12(s), respectively. Relative standard deviation (RSD) was lower than 16% for each perfluorinated compound. The results obtained showed that UHPLC–MS/MS and CLC–MS allow the determination of perfluorinated compounds in water samples with satisfactory sensitivity and resolution and reduced analysis time. Therefore, both techniques were employed for the analysis of water samples to determine the target analytes at low concentration levels and with lower analysis times than using HPLC–MS/MS. Similar statistical values were obtained from both techniques at 95% confidence level. Several compounds have been detected, but perfluorooctanoic acid (PFOA) (171ngL−1 and 148ngL−1 by UHPLC–MS/MS and CLC–MS, respectively) showed the highest concentration.