A method to correlate microstructure from cross-section transmission electron microscopy (TEM) investigations and transport properties of a single well characterized high-Tc artificial grain boundary junction is reported. A YBa2Cu3O7-δ 45° twist junction exhibiting the typical phenomenology of high-Tc Josephson weak links was employed. The TEM sample preparation is based on focused ion beam etching and allows to easily localize the electron transparent area on a microbridge. The reported technique opens clear perspectives in the determination of the microstructural origin of variations in Josephson junction properties, such as the spread in Ic and IcRN values and the presence of different transport regimes in nominally identical junctions. © 1999 American Institute of Physics.