The two major protease inhibitors in mouse plasma are a1-protease inhibitor (a,-PI), putative inhibitor of neutrophil elastase, and contrapsin, an inhibitor in vitro of trypsinlike proteases. We have shown by nucleotide sequence analysis that these two inhibitors are related (R. E. Hill, P. H. Shaw, P. A. Boyd, H. Baumann, and N. D. Hastie, Nature (London) 311: [175][176][177] 1984). Here, we show that the contrapsin and al-PI genes are members of two different multigene families, each containing at least three genes in mice and rats. We established the chromosomal locations of these genes by analyzing the segregation of restriction fragment length polymorphisms in recombinant inbred mouse strains. These experiments show that the multiple genes in each family are clustered and that the two gene families are closely linked on chromosome 12. Thus the genes for contrapsin and al-PI are likely to have evolved by duplication of a common ancestral gene. The contrapsin multigene family codes for multiple mRNA transcripts in the liver. There is a genetic difference among inbred mouse strains in the regulation of two of these transcripts. In some inbred strains the transcripts are synthesized constitutively; in others they are induced by inflammation. We mapped in recombinant inbred strains the regulatory locus responsible for this genetic variation and found it is linked to the contrapsin multigene family, which suggests a cis-acting regulatory element. We also found that the contrapsin and the a,-PI multigene families have acquired very different regulatory responses since the time of the gene duplication event.The two major mouse plasma protease inhibitors are a1-proteinase inhibitor (a,-PI; also called otl-antitrypsin) and contrapsin, which together are responsible for most of the trypsinlike inhibitory activity of mice (27, 28). These two inhibitors are synthesized by hepatocytes, and secretion from this cell type is primarily responsible for their high levels in plasma (3,4,21). Mouse a,-PI is homologous to (14) and appears to be functionally equivalent to human a1-PI; in contrast, contrapsin activity appears to be novel to rodents (27). At the nucleotide sequence level, however, the contrapsin gene is closely related to that encoding human plasma al-antichymotrypsin (ao-achy) (14). In addition, contrapsin and ao-PI are related to each other (59% nucleotide homology) but to a lesser extent than with their counterparts in humans (14).These inhibitors have been placed into a larger superfamily of proteins (sharing 29 to 34% amino acid homology with each member) which includes other protease inhibitors such as antithrombin III (7) as well as proteins with no known inhibitory activity, including chicken ovalbumin (15) and rat angiotensinogen (10). It is not known whether these members evolved from a common ancestral gene or are related through a process of convergent evolution (19). Genetic analysis of the chromosomal location of related genes may provide insight into their mode of evolution. Because a,-PI and contraps...