Inbred mice can be phenotypically divided into two groups: those that contain high levels of a kidney metallo-endopeptidase activity (meprin-a) and those with low meprin-a activity. In studies to investigate the molecular basis for the heterogeneity in the expression of this proteinase activity, we found a latent metallo-proteinase activity associated with kidney membranes of C3H/HeJ mice, a low activity strain. The latent proteinase was activated by treatment of kidney brush border membranes with trypsin and was purified from solubilized C3H kidney membranes. Purified preparations of the C3H latent proteinase (referred to as meprin-b) contained three major proteins of subunit molecular weights 90,000, 140,000, and 160,000. In the absence of reducing agents, four 90,000-Da subunits are covalently linked by S-S bridges. The two higher molecular mass proteins are not covalently linked to each other or to the 90,000-Da subunits. However, cross-linking and affinity chromatography studies indicated that the proteins in the meprin-b preparation were tightly associated. By contrast, purified meprin-a contains only 85,000-Da subunit proteins linked by S-S bridges to form a tetramer. Endoglycosidase F treatment decreased the mass of the 90,000-Da meprin-b subunit and the 85,000-Da meprin-a subunit to polypeptides of 65,000-70,000 Da. The 90,000- and 85,000-Da subunits are immunologically similar, in that polyclonal antibodies prepared against one of the subunits cross-react with the other. The substrate specificities and inhibitor profiles of purified preparations of meprin-a and meprin-b are also similar. These data are consistent with the proposition that meprin-b is a polymorphic form of meprin-a that is incompletely processed in vivo.