The effects of annealing on the electrical transport behavior of CoFe/MgO/CoFe magnetic tunnel junctions have been studied using a combination of site-specific in situ transmission electron microscopy and three-dimensional atom-probe tomography. Annealing leads to an increase in the resistance of the junctions. A shift in the conductance curve (dI/dV) minimum from 0 V for the as-grown specimen correlates with a sharply defined layer of CoFe oxide at the lower ferromagnetic interface. Annealing decreases the asymmetry in the conductance by making the interfaces more diffuse and the tunnel barrier more chemically homogeneous.