Genetic studies have shown that the induction of beta-glucuronidase in mouse kidney in response to androgens is under the control of the Gus-r gene, closely linked to the beta-glucuronidase structural gene, Gus-s, on mouse Chromosome 5. Despite the fact that a single structural gene codes for beta-glucuronidase, enzyme molecules show considerable charge heterogeneity, presumably as a result of post-translational events. Because the enzyme is a tetramer, this heterogeneity has complicated examination of the cis versus trans action of the Gus-r gene. In order to resolve the problem, we have developed a quantitative method for determining the amount of beta-glucuronidase derived from each structural allele in mice heterozygous for beta-glucuronidase electrophoretic mobility. The method involves separation and quantitation of genetically variant cyanogen bromide peptides from the enzyme. Using this technique, we show that Gus-r acts cis, suggesting that it directly affects the template activity of the glucuronidase structural gene.