Liver beta-glucuronidase is structurally altered in inbred strain PAC so that a peptide subunit with a more basic isoelectric point, GUS-SN, is produced. This allele of beta-glucuronidase was transferred to strain C57BL/6J by 12 backcross matings to form the congenic line B6 X PAC-Gus(n). Liver beta-glucuronidase activity was halved in males of the congenic strain compared to normal males. The lowered activity was specifically accounted for by a decrease in the lysosomal component. There was no alteration in the concentration of microsomal activity. This alteration in the subcellular distribution of beta-glucuronidase in Gus(n)/Gus(n) mice was confirmed by two independent gel electrophoretic systems which separate microsomal and lysosomal components. beta-Glucuronidase activity was likewise approximately halved in mutant spleen, lung, and brain, organs which contain exclusively or predominantly lysosomal beta-glucuronidase. The loss of liver lysosomal beta-glucuronidase activity was shown by immunotitration to be due to a decrease in the number of beta-glucuronidase molecules in lysosomes of the congenic strain. The Gus(n) structural alteration likely causes the lowered lysosomal beta-glucuronidase activity since the two traits remain in congenic animals. Heterozygous Gus(n)/Gus(b) animals had intermediate levels of liver beta-glucuronidase. Also, the effect was specific, in that three other lysosomal enzymes were not reproducibly lower in Gus(n)/Gus(n) mice. Gus(n) is, therefore, an unusual example of a mutation which causes a change in the subcellular distribution of a two-site enzyme.