Objective. To evaluate the regulatory potential of genetic loci controlling Mycobacterium butyricum adjuvant-induced arthritis (Mbt-AIA) using mono-and polycongenic rats.Methods. Of 4 quantitative trait loci (QTLs) that regulate Mbt-AIA, F344 alleles at 3 of these loci, Aia1, Aia2, and Aia3, are associated with lower arthritis severity, whereas F344 alleles at Aia4 are associated with greater arthritis severity. In this study, we constructed congenic lines by transferring 1 or more of the F344 genomic segments containing Aia1, Aia2, and Aia3 onto the DA genome. We comparatively evaluated their responses to Mbt-AIA with the responses of parental DA and F344 rats.Results. Aia1, encompassing the rat major histocompatibility complex, reduced arthritis severity in monocongenic rats of both sexes. The arthritis-lowering effects of Aia2 and Aia3 were sex-influenced and were therefore observed in only males and only females, respectively. Polycongenic rats containing F344 genomic regions at Aia1, Aia2, and Aia3 developed Mbt-AIA of relatively greater severity than did F344 rats, implying that in DA and F344 rats, there could be other Mbt-AIA loci in addition to Aia1, Aia2, Aia3, and Aia4. To test the possibility that some of these Mbt-AIA-regulatory loci may colocalize with other arthritis QTLs, we evaluated Mbt-AIA in DA.F344 monocongenic rats containing collagen-induced arthritis QTLs. Cia5 (the QTL region on chromosome 10), but not Cia5a, Cia4, or Cia6, also regulated Mbt-AIA, and was named Aia5.Conclusion. F344 genomic regions at Aia1, Aia2, and Aia3 and the newly identified Aia5 contain genes that reduce Mbt-AIA severity in DA rats. These Mbt-AIA-regulatory loci overlap rheumatoid arthritissusceptibility loci in humans.Rheumatoid arthritis (RA) is a polygenic autoimmune disease characterized by chronic inflammation in the joints that eventually leads to destruction of the underlying bone and cartilage (1). Difficulty in defining the etiopathology of RA from various clinical, physiologic, and biochemical studies has motivated the application of genetic approaches to RA (2,3). Identification of genes that regulate RA in humans should reveal the primary physiologic mechanisms underlying RA, thereby clarifying disease pathogenesis, identifying path- ways and targets for therapeutic intervention, and providing an opportunity for preclinical diagnosis. From studies on twins, there is evidence of a genetic influence on RA (4). Recent genome-wide linkage analyses in humans have confirmed the existence of both major histocompatibility complex (MHC) and non-MHC genes that regulate RA (5-7). However, studies aimed at identifying the causative genes in a polygenic disease such as RA are complicated by multiple environmental and demographic factors (8,9). Population heterogeneity is also a concern in genetic studies with humans (8).A valuable alternative approach is to study the genetic regulation of experimentally induced forms of arthritis in rats, wherein the complications of genetic heterogeneity and environmental influence...