Autoimmune diseases, such as type 1 diabetes (T1D), result from a break in immune tolerance leading to an attack on self-antigens. Autoantibody levels serve as a predictive tool for the early diagnosis of T1D. Interestingly, in 3A9 TCR:iHEL transgenic mouse model, high autoantibody levels also correlate with susceptibility to autoimmune diabetes. In other autoimmune models, autoantibody production is associated to a locus on mouse chromosome 12. In an attempt to understand the genetic regulation of autoantibody production and their contribution to autoimmune susceptibility, we generated a NOD.H2k congenic strain bearing B10 alleles at the D12Mit184-D12Mit12 locus, named NOD.H2k_Chr12. In these congenic mice, we assessed the quantity and affinity of auto-antibodies compared to that of NOD.H2k littermate controls. In the NOD.H2k_Chr12 congenic strain, we observed a significant decrease in both IgG1 autoantibody levels and in their affinity. These results demonstrate that a genetic polymorphism present within the Chr12 locus regulates the production of autoantibodies. Of importance, the global humoral response was not impaired in terms of quantity, but only in terms of affinity in our congenic mice. In agreement with a potential pathological role of IgG1 autoantibodies in the 3A9 TCR:iHEL transgenic model, NOD.H2k_Chr12 mice exhibited a reduced susceptibility to autoimmune diabetes. In conclusion, by analyzing a locus on mouse chromosome 12, we observe phenotypes linking diabetes susceptibility, autoantibody production and antibody affinity. Future work will investigate candidate genes comprised within the interval, thereby contributing towards better defining genetic regulation of autoimmunity associated to humoral response.