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Proton conducting oxides such as BaCe0.9Y0.1O3−δ have considerable promise for intermediate temperature fuel cells. Unfortunately these tend to be unstable, e.g. to attack by carbonation. Previous work has highlighted the possibility of utilising barium zirconate to provide a chemically stable electrolyte; however such materials are difficult to sinter yielding very high overall resistances. Whilst this sintering problem is soluble, there are still very significant questions about the intrinsic grain conductivity, which varies by orders of magnitude for different reports. Here we demonstrate that there are two variants of BaZr0.9Y0.1O2.95, both with the cubic perovskite structure. The α-form exhibits a slightly smaller unit cell and much lower protonic conductivity than the β-form. The α-form is observed in better equilibrated samples and neutron diffraction demonstrates that this difference originates in a small degree of cross substitution of the Y atom onto the A-sites for the β-form, suggesting a novel approach to enhance ionic conductivity by reducing defect association through A-site substitution.