Methods using a sequence of externally generated magnetic fields to initialize the magnetization directions of each of the layers in perpendicular MTJ MRAM elements for data and reference bits when the required magnetization directions are anti-parallel are described. The coercivity of the fixed pinned and reference layers can be made unequal so that one of them can be switched by a magnetic field that will reliably leave the other one unswitched. Embodiments of the invention utilize the different effective coercivity fields of the pinned, reference and free layers to selectively switch the magnetization directions using a sequence of magnetic fields of decreasing strength. Optionally the chip or wafer can be heated to reduce the required field magnitude. It is possible that the first magnetic field in the sequence can be applied during an annealing step in the MRAM manufacture process.