Understanding the molecular regulation of immunoglobulin A (IgA) expression is important as it plays an essential role in the first-line defence through mucosal secretions. Using inbred mouse strains, we identified two independent and dominant acting genetic loci that synergistically cause a 40-fold upregulation in serum IgA levels when introduced into the murine strain C57Bl/6J (B6). The first locus on chromosome 12 appears to be mainly responsible for the natural four-fold higher IgA levels in C3HeB/FeJ (C3H) compared to B6 mice. A second independent, chemically induced mutation on chromosome 5 caused a two-fold elevation when transferred from C3H into B6 mice. Both loci in concert effect a 40-fold elevation against the B6 genetic background. We determined the chromosomal localization of the two loci simultaneously by a one-step mapping process. The chemically induced mutation was identified within the immunoglobulin joining chain (IgJ) gene on chromosome 5. The major serum IgA modifier between the C3H and B6 was located on chromosome 12. This modifier region was mapped to a 350 kb region containing several immunoglobulin heavy-chain genes and the Igα germline switch gene. We speculate that by interfering with both IgA expression and distribution, synergistic regulation of IgA is achieved.