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Fuel cells (FCs) are among the more efficient solutions to limit the emission of greenhouse gases. Based on the conversion of the chemical energy of a fuel (often hydrogen) and an oxidizing agent (often oxygen) into electrical energy, a typical FC produces a voltage of 0.7 V under load. The potential is highly increased by placing the cells in series to obtain a stacked cell. Among the types of FCs, the polymer electrolyte membrane FCs (PEMFCs) are developed mainly for transport applications, because of their low impact on the environment, high power density and light weight compared with other types of FCs. Phosphoric acid (H3PO4) doped polybenzimidazole (PBI) membranes are widely used as efficient electrolytes. The performance of a (high temperature, 130–200 °C) HT-PEMFC depends mainly on the amount of H3PO4 in the solid polymer membrane. The strong autoprotolysis of H3PO4 is responsible for the high proton conductivity also in the anhydrous state. In this study, the H2OH3PO4 system is investigated in the temperature range 60–150 °C with varying water vapour activity at constant atmospheric pressure. Main purpose is to gain more insights into the kinetics of the equilibria in the H2O-H3PO4 system, which influence the fuel cell performance. Density, water content, electrical conductivity and activation energy are determined by exposing H3PO4 solutions for sufficiently long periods to controlled gas atmosphere in order to reach near-equilibrium conditions. The coexistence of ortho- and pyrophosphoric acid is analysed and higher condensed species are also considered. A new setup fully made in quartz is designed and developed to mix the phosphoric acid solutions in a climate chamber. The experimental results are compared to literature data to validate the developed setup and the methodology.