The insulin minisatellite or variable number of tandem repeats locus (INS VNTR) is the best candidate for the type 1 diabetes mellitus (T1DM) susceptibility locus IDDM2. Small class I alleles associate with predisposition to T1DM, whereas large class III alleles associate with dominant protection. We have analysed variant repeat distribution within the minisatellite and combined this with flanking haplotypes to define five new ancestral allele lineages. Class III alleles divide into two highly diverged lineages, IIIA and IIIB, which correspond perfectly to the previously defined Protective (PH) and Very Protective (VPH) haplotypes, respectively. Class I alleles are divided into three newly defined lineages, IC+, ID+ and ID-, by a combination of variant repeat distributions and flanking haplotypes. All class I alleles are equally predisposing to T1DM except for ID- alleles which are protective when transmitted from ID-/III heterozygous fathers. Similar results have been previously reported for alleles of 42 repeats in length (allele 814) which represent a subset of the ID- lineage. Division of class ID- alleles into those of 42 repeats and those of other sizes suggested that this protective effect was a feature of all ID- alleles, irrespective of size. ID- alleles are only clearly distinguished from all other alleles by an MSPI(-) variant within IGF2 downstream of the minisatellite, suggesting that the apparent role of the minisatellite in susceptibility to T1DM may be modified by neighbouring haplotype and therefore that IDDM2 could have a multi-locus aetiology.