The atomic structure of the interfaces of Josephson junctions formed by epitaxial YBa2Cu3O7/PrBa2Cu3O7/YBa2Cu3O7triple‐layer films was investigated by high‐resolution transmission electron microscopy. The samples were fabricated by sputter deposition on surfaces which were etchedexsitueither chemically, using a nonaqueous Br‐ethanol solution, or by an Ar ion beam. In the interfaces produced after ion etching a thin intermediate layer with a thickness of a few nanometers was observed. The main part of this layer consists of cubic PrBa2Cu3O7or YBa2Cu3O7which is cation disordered. The interfaces formed during deposition on Br‐ethanol‐etched surfaces did not contain such an intermediate layer but exhibited high structural perfection similar to that of interfaces producedinsitu. These observations permit a qualitative explanation of the difference in the electrical properties of junctions produced by these two techniques. ©1995 American Institute of Physics.