The fourth component of human complement is encoded by two separate, but closely linked, loci, C4A and C4B, that have been positioned within the class III region of the HLA complex. While the two isotypes vary by only six amino acid residues, they differ significantly in haemolytic activity. Both loci are considerably polymorphic and this may be biologically relevant to ensure interaction with a wide range of pathogens. The number of C4 genes expressed is polymorphic as null alleles, total deficiency and duplication has been shown based on protein studies. Southern analysis of 24 different haplotypes with either C4A or C4B null alleles using the C4 probes showed that three of the null alleles were due to deleted genes but the majority appeared normal. A cosmid library was prepared from DNA of one of the deleted haplotypes and the region of deletion analysed by restriction mapping.