The structure of as‐deposited and annealed Cr/GaAs Schottky contacts was investigated by high resolution and analytical electron microscopy. The Schottky barrier height for contacts prepared by cleavage andinsitumetallization in ultrahigh vacuum was stable upon annealing up to 370 °C in N2. In contrast, the contacts prepared on air‐exposed substrates show an increase of the barrier height by 80 meV during annealing in the same range of temperatures. Comparing these two types of contacts, distinct differences in the grain size, presence of an oxide layer at the interface, and change in stoichiometry in the substrate beneath the contact were detected.