In-situ heating fluctuation electron microscopy and scanning transmission electron microscopy have been utilized to study compositional and structural heterogeneities in Zr 51 Cu 32 Al 9 Ni 8 thin films upon annealing. Composition fluctuations are present in the as-deposited thin films. Well below the glass transition temperature, the composition fluctuations increase with annealing time. Short- and medium-range order also change with annealing temperature. The observed heterogeneities in the glass structure persist until annealing causes crystallization. The 20nm thick Zr 51 Cu 32 Al 9 Ni 8 films contain oxide layers both at the surface and the film/substrate interface with the total thickness of 7–8nm. In-situ annealing increased the oxygen content of the whole films to about 24wt.% after 2h at 400°C.