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. Two-point 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 = 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.