Long side chain perfluorosulfonic acid (PFSA) aqueous solutions with various degrees of substitution and trifluoroacetic acid solutions were investigated by liquid F-19 nuclear magnetic resonance (NMR) to propose a new and efficient quantification protocol. These two examples were selected to respond to a specific need for quantification in fuel cell applications. Classical quantification revealed a systematic underestimation of the PFSA concentrations at room temperature, in contrast to small fluorinated molecules. Dynamic light scattering data suggested the presence of NMR silent aggregates up to 50 degrees C. These aggregates appeared as large particles of about 30 mu m in diameter, resulting from the agglomeration of primary aggregates through hydrogen bonds. An increase of the measurement temperature to 80 degrees C was sufficient to take apart the secondary aggregates, and get the correct quantification. In parallel, a rapid F-19 NMR quantification method was developed using a careful analysis of the Signal-to-Noise ratio. This new method provided, in at least a six decades range, an estimation of the PFSA concentration without the need for an external reference. This approach may be successfully applied to determine the fluorine atom content of any small molecule or polymer. (c) 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016, 54, 2210-2222