The crystalline structure, chemical composition, and bonding states across epitaxial Fe/MgO/Fe001 mag-netic tunnel junctions grown by molecular-beam epitaxy have been investigated down to the atomic scale by spatially resolved electron energy-loss spectroscopy. Both metal-insulator interfaces exhibit significant rough-ness, which can be attributed to Fe and MgO terraces overlapping one another. These terraces extend over typical widths of 6–10 nm parallel to the interface and over typical heights below 1 nm, and a structural asymmetry of the roughness is revealed. These features could be responsible for the nonsymmetrical transport properties measured when reversing the applied voltage.