Abstract: The microstructure of YBCO/SrRuO3/YBCO junctions in the edge geometry have been studied by high resolution electron microscopy. Various defects in the YBCO and SrRuO3 films are observed and analyzed. The most striking defects in the c-axis-oriented YBCO film are a-axis particles, which cause bending and interruption of lattice planes as well as high steps and cracks in the subsequent layers. The SrRuO3 layer in the ramp-edge junction region consists of small domains with slightly different orientations. This leads to the formation of steps on its surface and large variation in SrRuO3 thickness. Mechanisms for forming this defective layer are suggested based on the growth mode and the crystal structure of SrRuO3. We find evidence for strain fields at the SrRuO3/YBCO interface. The oxygen deficiency in YBCO caused by this interface strain may to a large part be responsible for the excess resistivity of this junction. In addition to the defective SrRuO3 layer, the occurrence of various defects in the junction area, including Y2O3 and a-axis YBCO particles, seem to be the cause for the wide scatter in the junction electrical characteristics. The formation of steps and large thickness variation in the barrier layer may be the reason for the rather large critical thickness of the SrRuO3 superconductor-normal-superconductor (SNS) junction. In addition to the junction interfaces, the microstructure of SrRuO3/LaAlO3 and SrRuO3/SrTiO3 interfaces have also been studied.