We have developed a new in situ preparation process for trilayer structures of vertically-stacked Josephson junctions. We adopted YBa2CU3O7-x, (YBCO) as a base electrode, and YbBa2CU3O7-x (YbBCO) as a counter electrode in these junctions. The barrier was formed by sputtering in a reduced total gas pressure and subsequent annealing. As the gas pressure decreases, the mean free path of the negative ions increases, which results in the bombardment of higher energy ions to the substrate and in etching the base electrode surface. The critical current Ic of the obtained junction was modulated up to 50% by applying an external magnetic field. The difference of the characteristics between the junctions fabricated by this new technique and conventional interface-treated junctions would be attributed to the difference in the species and their energy distributions of the particles incident to the sample during the barrier formation. (c) 2006 Elsevier B.V. All rights reserved.