Objective. Constitutional structural chromosomal rearrangements (CSCRs) have facilitated the identification of genes associated with early-onset monogenic disorders and, more recently, genes associated with common and late-onset disorders. In an attempt to find genetic clues to their etiologies, we studied the risk of autoimmune diseases in a Danish cohort of CSCR carriers.Methods. We followed up 4,866 CSCR carriers over 71,230 person-years (1980 through 2004) for autoimmune diseases recorded in the Danish Hospital Discharge Register. Standardized incidence ratios (SIRs) and 95% confidence intervals (95% CIs) served as measures of the relative risk. To identify possible candidate loci for autoimmune diseases, the reported chromosomal breakpoints and deletions in CSCR carriers who developed autoimmune diseases were compared with previously suggested loci for these diseases.Results. The overall risk of any autoimmune disease among CSCR carriers was inconspicuous (SIR 1.2 [95% CI 0.95-1.5]; n ؍ 74 cases observed versus 61.3 expected), but carriers of rearrangements involving chromosomes 2, 19, and 21 were at significantly increased risk. For the specific autoimmune diseases studied, cohort members were at significantly increased risk of Dupuytren's contracture, pernicious anemia, and juvenile rheumatoid arthritis (JRA). Sixteen carriers who developed an autoimmune disease had a chromosomal breakpoint or deletion coinciding with a previously suggested locus, including deletions 18p11, 18q22, and 22q11 associated with JRA.Conclusion. CSCR carriers do not have a generalized predisposition to autoimmune diseases. However, we confirmed a number of reported susceptibility loci for JRA, and we suggest new susceptibility loci on chromosomes 5 and 11 for Dupuytren's contracture, and 19p13 as a possible shared susceptibility locus for a range of autoimmune diseases.Autoimmune diseases are a complex group of chronic diseases characterized by the loss of immune tolerance to self antigens. The etiology of most autoimmune diseases is unknown, but genetic risk factors, including the major histocompatibility complex (MHC), are believed to be involved together with environmental factors (1). The MHC and some of the non-MHC susceptibility genes are suggested to be shared by different autoimmune diseases, which might possibly explain the occasional observation of different autoimmune diseases within the same family and individuals with several different autoimmune diseases (2).To date, strategies for identifying genes associated with complex diseases have been based primarily on the mapping of susceptibility loci by linkage and association studies. The inherent difficulties of these approaches are due to the genetic heterogeneity associated with complex disorders, families with few affected members, incomplete penetrance, variable age at onset, and difficulties associated with diagnostic criteria. In monogenic disorders, a fruitful alternative approach has been to identify affected individuals with unique chromosomal rearrangements...