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It has been long-recognized that carbonation of anion exchange membrane fuel cells (AEMFCs) would be an important practical barrier for their implementation in applications that use ambient air containing atmospheric CO 2 . Most literature discussion around AEMFC carbonation has hypothesized: (1) that the effect of carbonation is limited to an increase in the Ohmic resistance because carbonate has lower mobility than hydroxide; and/or (2) that the so-called “self-purging” mechanism could effectively decarbonate the cell and eliminate CO 2 -related voltage losses during operation at a reasonable operating current density (>1 A cm −2 ). However, this study definitively shows that neither of these assertions are correct. This work, the first experimental examination of its kind, studies the dynamics of cell carbonation and its effect on AEMFC performance over a wide range of operating currents (0.2–2.0 A cm −2 ), operating temperatures (60–80 °C) and CO 2 concentrations in the reactant gases (5–3200 ppm). The resulting data provide for new fundamental relationships to be developed and for the root causes of increased polarization in the presence of CO 2 to be quantitatively probed and deconvoluted into Ohmic, Nernstian and charge transfer components, with the Nernstian and charge transfer components controlling the cell behavior under conditions of practical interest.