IDDM9-region on chromosome 3q has shown suggestive evidence for linkage to type 1 diabetes in some but not all genome scans. We analyzed 22 microsatellite markers in 121 Finnish type 1 diabetes multiplex families across the IDDM9-region. Twopoint maximum LOD scores of 3.4 and 2.5 were detected with markers D3S1589 and D3S3606, respectively. Two markers were further tested for association using the transmission disequilibrium test in 384 Finnish type 1 diabetes simplex families. Marker AFM203wd10 showed association with type 1 diabetes (P ¼ 0.0002 for allele R16). Association was present in families with children carrying the HphI-23 AA risk genotype at IDDM2 but not in families with children carrying protective AT or TT genotypes implying interaction between the two loci. Our data gives credence to earlier findings of linkage in this region and suggests a location for a polymorphism affecting type 1 diabetes susceptibility in the area surrounding AFM203wd10. Genes and Immunity (2006) Keywords: Type 1 diabetes; linkage study; Finnish population; IDDM9; multifactorial inheritance HLA-region genes DQB1-, DQA1-and DRB1 are the major loci (IDDM1) in type 1 diabetes (T1D) susceptibility, where several predisposing and protective alleles and haplotypes have been reported. The HLA-region explains approximately 50% of the genetic background of T1D suggesting additional genetic determinants. In addition to the HLA loci, several candidate genes and regions have been assigned to T1D in numerous wholegenome scans and candidate gene studies. We have tested one of these regions, IDDM9, 1 for linkage and association in the Finnish population. Linkage evidence for the IDDM9-region so far is inconclusive, as only suggestive linkage has been reported. The highest unconditioned maximum LOD score (MLS) (1.1) was reported in a study of 356 UK families 1 but the majority of evidence for this region has come from data sets stratified by HLA status or sex. Davies et al. 2 reported an MLS of 1.9 for the marker D3S1303 in sibpairs sharing two HLA alleles identical by descent (IBD). An MLS of 2.4 was observed in a subset of 126 HLA-identical HLA-DR3/DR4 heterozygous sibpairs. 1 Furthermore, an MLS of 2.0 was seen in female sibpairs in the same UK data set using marker D3S1279. 3 A nominal LOD score of 1.05 was observed for 107 Finnish T1D sibpairs at a region located B30 cM upstream of IDDM9 in our earlier study. 4 The region spans B2 cM between markers D3S3620 and D3S3576 and contains an autoimmune candidate locus, the CD86 gene, which is a costimulatory molecule involved in T-cell activation and proliferation via interaction with the T-cell ligands CD28 and CTLA4 (cytotoxic T-lymphocyte-associated antigen 4). An association study of two CD86 SNPs in the Finnish population showed no significant association with T1D 5 implying that CD86 is not the alleged T1D susceptibility gene in this region.In the present study we reanalyzed the IDDM9 region using 22 microsatellite markers in a region spanning 60 cM around the reported IDDM9-region at ...