The relaxation of the interface structure of Fe/MgO͑100͒ magnetic tunnel junctions predicted by densityfunctional theory depends significantly on the choice of exchange and correlation functional. Bader analysis reveals that structures obtained by relaxing the cell with the local spin-density approximation ͑LSDA͒ display a different charge transfer than those relaxed with the generalized gradient approximation ͑GGA͒. As a consequence, the electronic transport is found to be extremely sensitive to the interface structure. In particular, the conductance for the LSDA-relaxed geometry is about 1 order of magnitude smaller than that of the GGArelaxed one. Surprisingly, the effect of the exchange and correlation potential within both the LSDA and the GGA has a little effect on the calculated transmission coefficient when applied to the same Fe/MgO/Fe ͑001͒ geometry. The high sensitivity of the electronic current to the details of the relaxed interface might explain the discrepancy between the experimental and calculated values of magnetoresistance.