C1r and C1s are distinct, but structurally and functionally similar, serine protease zymogens responsible for the enzymatic activity of the first component of complement (C1). Recent comparisons indicate a significant degree of sequence similarity between C1r and C1s and support the hypothesis that they are related by gene duplication. Complementary DNA probes for human C1r and C1s do not cross-hybridize even at mild stringency conditions and are therefore gene-specific. Using a panel of 25 human-rodent cell hybrids, we have independently assigned the C1r and the C1s genes to chromosome 12. In situ hybridization analyses were consistent with these assignments, showing in addition that both C1r and C1s are located on the short arm of the chromosome in the region p13. These data suggest that the homologous C1r and C1s genes have remained closely linked after duplication of a common ancestor. The C1r and C1s loci also provide useful polymorphic DNA markers for the short arm of chromosome 12.