The third component of the human C system, C3, exhibits two common genetic variants. These variants have been characterized by high voltage agarose electrophoresis and are designated C3 fast (C3F) and C3 slow (C3S). C3F occurs at appreciable frequencies only in Caucasian populations and has been shown to be associated with an increased incidence of certain diseases, such as partial lipodystrophy, IgA nephropathy, and Indian childhood cirrhosis. It has been shown that C3F differs from C3S with regard to isoelectric point as well as its ability to bind macrophages. The availability of a full-length cDNA probe for human C3 has made it possible to study the polymorphism at the genomic level. We have used RNA/RNA hybridization to demonstrate that the difference between C3F and C3S occurs in the C3d region. We subsequently used oligonucleotide-primed DNA amplification to show that C3F arises from a point mutation at codon 1216 converting a deoxyadenosine for a deoxyguanosine. The result of this point mutation at the translational level is the substitution of an asparagine residue in C3S for an aspartic acid residue in C3F. It is known that C3d contains the binding site for CR2 as well as the internal thioester site and multiple protease cleavage sites. The identification of the structural basis of the differences between C3F and C3S will assist our continuing studies of the mechanism of the functional differences between the two alleles and the disease associations of C3F. It also allows us to use DNA based techniques to allotype C3 in subjects with little or no C3 in their serum.