We report results obtained from several hundred Nb/Al2O3/Nb tunnel junctions fabricated by the ‘‘whole‐wafer’’ process. These results indicate that one of the factors determining resistance and quality variations in such devices is the microstructure of the underlying base layer of niobium. We have further developed the technique of anodization spectroscopy to provide a quantitative measure of the variation in the thickness of the thin aluminum layers which contain the tunnel barrier and have related this to the temperature at which the niobium base layer is deposited. We show that at least two mechanisms are responsible for normal‐state resistance variations in such devices and that device quality is closely related to the integrity of the aluminum layer underlying the tunnel barrier.