A method has been developed to measure 29 perfluorinated acids (PFAs) including short-chain perfluorocarboxylates (PFCAs) such as trifluoroacetic acid (TFA; C2) and long-chain PFCAs, perfluoroalkylsulfonates, fluorotelomer acids, and two perfluorooctylsulfonamides in water matrices. The method involves solid phase extraction (SPE) using a weak anion-exchange (WAX) cartridge, an ion-exchange high-performance liquid chromatography (HPLC) column separation, and tandem mass spectrometry (MS/MS) detection. To our knowledge, this is the first HPLC-MS/MS method to determine TFA in water at sub-ng L(-1) concentrations. The method is selective, simple, and robust, capable of measuring 29 PFAs in a single analysis, with overall recoveries of the target analytes ranging from 75% to 132%. The method was applied to the analysis of rainwater samples collected from two cities in Japan. TFA and several short-chain PFAs were the major compounds found in rainwater.