Major histocompatibility complex (MHC) plays a largely predominant role in the genetic predisposition to type 1 diabetes, in both humans and rodents. While class II loci have long been recognized as essential, they do not fully explain the MHC-linked genetic component of type 1 diabetes. In the present study, using new NOD congenic strains harboring defined chromosomal segments from C57BL/6 mice, we circumscribed three distinct loci influencing murine type 1 diabetes and tightly linked to but separated from the class II region. Our findings might guide the search for additional HLA-linked loci in human type 1 diabetes.