Atom probe tomography (APT) and transmission electron microscopy (TEM) are used to characterize MgO-based magnetic tunnel junctions in as-deposited and annealed states. The annealing produced giant tunneling magnetoresistance (TMR) values of ∼350%. Upon annealing, Mn diffuses from an IrMn exchange bias layer within the device to one interface of the tunnel barrier layer, while the TMR initially increases. TEM and APT show that Mn does not appear to diffuse into the MgO barrier, but segregates at the CoFe/MgO interface. © 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.