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We are investigating device yield in our Nb-nine-layer fabrication process for single-flux-quantum (SFQ) circuits, in which the critical current density of the Nb/AlOx/ Nb Josephson junction (JJ) is 10 kA/cm2 and the minimum JJ size is 1 μm2. We fabricated several shift registers (SRs) with different sizes that exhibit bit capacities from 16 to 2560 bits on a chip on many wafers. The SR yields correlate roughly with process defect test results using diagnostic chips, which are included in all wafers and consist of various diagnostic patterns such as for interlayer and intralayer insulations. When the defect number was above a certain level, the SR yield drastically degraded. The other reason of SR yield degradation is poor size uniformity of JJ patterns. The JJ pattern resolutions using our i-line stepper depend on the several-μm-level flatness of wafers. All SRs on a chip consisting of 68 990 JJs operated correctly. We obtained both “good” and “poor” chips without intentional changes of process conditions. The “poor” chip was strongly affected by magnetic flux traps. We believe that determining the cause of this difference is key to fabricating SFQ circuits consisting of 100 000 or more JJs.