The microstructure of various types of Josephson junctions is investigated with cross-sectional (CS) high-resolution electron microscopy (HREM). Special specimen preparation techniques, to facilitate the CS investigation, are discussed in the first part. Examples are shown of specially produced arrays of junctions and of the focused ion beam thinning technique allowing us to investigate specific measured junctions. Ramp-type junctions with (PrBCGaO) barrier layers are discussed in more detail in the second part. The microstructure of PrBCGaO (0.1 < x < 1.0) thin films, barrier layers and bulk material is studied by HREM. Thin barrier layers with contain a Ga-rich intergrowth, never observed before in YBCO-type structures. Ga-rich inclusions in single thin films exhibit a similar structure. In addition, diffusion of Ga in the ion-etched substrate surface region was observed. The observed segregation of Ga from the PrBCGaO barrier layer explains the observed junction properties.