Mouse complement component C1q is a serum glycoprotein which consists of six A chains, six B chains and six C chains. The three polypeptides are 223, 228, and 217 residues long, respectively, and are encoded by three genes. DNA probes for mouse C1q A, B, and C chains were hybridized to Southern blots of DNA obtained from various inbred mouse strains. On the basis of fragment length polymorphisms, two different alleles of each of the genes could be identified. The distribution of these alleles was determined in the BXD and LXPL recombinant inbred strain series. Comparison with previously reported strain distribution patterns shows that the genes encoding mouse C1q map to the same locus on distal chromosome 4. Overlapping clones spanning the entire gene cluster of C1q were isolated from genomic libraries using specific cDNA probes. The three genes C1qA, C1qB, and C1qC are closely arranged on a 19 kilobase stretch of DNA in the 5' to 3' orientation A-C-B. Each gene consists of two exons separated by one intron. Sequence comparison of C1q from three different species have shown that the B chains have the strongest similarity. Southern blot analysis of chromosomal DNA from 14 vertebrate species demonstrated highest similarity between the C1qB genes, followed by C1qC and finally C1qA.