To establish the structural origins of the perpendicular magnetic anisotropy in Co-Pt alloys, a variety of magnetic and structural characterization techniques have been utilized. We have determined that the development of out-of-plane magnetization in these alloys, strongly depends on growth temperature and in contrast to CO/Pt Multilayers, the highest anisotropics and coercivities are observed in polycrystalline alloys with negligible preferred crystallographic orientation. Lattice strain Measurements, surface roughness determination and crystal growth studies indicate that contributions from magnetostrictive and magnetostatic contributions to the perpendicular anisotropy in these alloys are not significant. H RTEM and synchrotron-based x-ray diffraction experiments, on the other hand, confirm the existence of ordered CoPt3 at elevated temperatures. We suggest that the strong temperature dependence of the perpendicular anisotropy is correlated to the onset of spontaneous chemical ordering during the growth which results in anisotropie pair ordering. A tentative model explaining this strong temperature dependence is described.