Antiferromagnets (AF) such as MnPt and MnNi can be used in spin valves and tunnel junctions due to their high exchange coupling, high blocking temperature, and fair corrosion resistance. They are used as pinning layer in a AF/FM/barrier/FM structure, where FM is a ferromagnet such as CoFe and the barrier is an ultra-thin insulating layer. However, as deposited MnPt and MnNi films with thickness around 20 nm are in the fcc phase, and show no exchange bias in AF/FM bilayers. A transition from fcc to fct is required, and takes place upon annealing. We present an X-ray diffraction study of the phase transition in glass/Ta 7nm/Ru 3 nm/MnPt 20 nm/CoFe 5 nm/Ta 3 nm AF/FM bilayers. We observe the MnPt phase transition from fcc to fct around 250°C. We correlate the phase transition with the change of the bilayers magnetic properties.