The source of perpendicular anisotropy (PA) in 0.05 μ thick, evaporated amorphous GdCo films was investigated by correlating the magnetic domain structure, as observed in the Lorentz mode with film structure, as observed with high resolution electron microscopy and diffraction, as functions of post deposition in situ anneal and elevated substrate temperature. A strong void network was found to anneal out above 500°K at an apparent glass transition. PA was developed either together with this or at slightly higher temperatures and could be correlated to the appearance of 60-100 Å wide columnar arrays of two separate amorphous phases. The phase separation is evident also in a splitting of the single broad diffraction peak, normally observed in homogeneous amorphous deposits without PA, into two distinct components. Deposition at substrate temperatures above this glass transition results in amorphous films which crystallize on annealing without development of PA. From this, PA is thought to arise from anisotropically shaped Co-rich regions in a transition stage between the homogeneous amorphous and crystalline states.