Scanning Auger electron spectroscopy and scanning electron microscopy have been used to investigate the local composition and structure of highly textured axis oriented YBaCuO films with thicknesses in the range 0.4–1 μm. The cuprate films were sputtered on MgO and sapphire (100)-oriented single-crystal substrates at room temperature followed by several anneal stages below or at 920°C in pure oxygen. The YBaCuO/sapphire sample was examined again after an additional 750°C air anneal for 24 h. By applying Auger line profiling on a freshly prepared cross-sectional surface of a thin cuprate film deposited on a sapphire substrate we have been able to show that barium aluminate segregation at grain boundaries is the main cause of the higher electrical resistance usually observed for cuprate films on Al2O3. The (drastic) reduction in Tc can be attributed to the substitution of aluminium in the cuprate at copper sites. Severe interdiffusion has been observed for the epitaxial c axis oriented YBaCu oxide films grown on an MgO substrate, which leads to a deterioration in the superconductivity. The main reason for reduced Tc and quality of cuprate films on MgO is the copper loss into the substrate, the depth of penetration of copper extending more than 400 nm below the YBaCuO---MgO interface. From our experimental results it is evident that Auger line profiling is an important tool in the analysis of high Tc superconducting thin films.