Abstract The aim of this work is the fabrication of heterostructures of epitaxial oxides and metals for device applications. The epitaxial metals are deposited on R-plane sapphire substrates by dc magnetron sputtering in a linked UHV system. The oxide layer is then grown on top of this metal layer in a linked UHV pulsed laser deposition (PLD) system using a pulsed oxygen jet to provide oxidation of the ablation products while minimising oxidation of the metal layer. Isolating the oxide deposition from the metal deposition avoids contamination of the sputtering process which enables, very high quality, single crystal metal films to be produced. In this preliminary study the length of the oxygen pulse was varied during the initial growth of MgO on Nb to investigate when the epitaxial oxide nucleation became significantly degraded. The full width half maximum (FWHM) of the X-ray diffraction rocking curve was used as a gauge of the quality of the epitaxy (Nb: 0.33 °–0.92 °; MgO: 0.81 °–3.43 °). The results suggest that oxidation of the surface of the metal does indeed affect the epitaxy of the MgO overlayer with an oxygen pulse length greater than 3ms. The purity of the metal base layers was examined by residual resistance ratio (10 K to 293 K) and found to be in the range of 75 for a clean Nb film to 1.1 for a heavily oxidised Nb film.