Computer simulation is used to examine the size and relative Co layer thickness dependence of the magnetization flop in magnetic tunnel junctions with the structure NiFe(I)(7.5 nm)/AlOx (0.7 nm)/Co(I)(y nm)/Ru(0.7 nm)/Co(II)(7-y nm)/FeMn(10 nm). The flop angle, which was obtained at a typical sputtering condition from an energy minimization, increases with the increase of y. The unidirectional pinning reduces the magnetization flop and its effect is greater when the Co thickness difference is smaller due to a larger energy contribution from the pinning term. Magnetoresistance hysteresis loops of “as-sputtered” samples, which were subjected to the magnetization flop, are found to vary significantly with the relative Co layer thickness, the cell size, and the magnitude of the unidirectional pinning. © 2002 American Institute of Physics.