An improved microfabrication technique for Josephson junctions in superconducting integrated circuits, based on the use of a double-layer lithographic mask for partial anodization of the side-walls and base electrode of the junctions. The top layer of the mask is a resist material, and the bottom layer is a dielectric material chosen so to maximize adhesion between the resist and the underlying superconducting layer, be etch-compatible with the underlying superconducting layer, and be insoluble in the resist and anodization processing chemistries. The superconductor is preferably niobium, under a silicon dioxide layer, with a conventional photoresist or electron-beam resist as the top layer. This combination results in a substantial increase in the fabrication yield of high-density superconducting integrated circuits, increase in junction uniformity and reduction in defect density. A dry etch more compatible with microlithography may be employed.