Genetic studies of malnutrition-related diabetes are few. We have analyzed the HLA class II gene polymorphism in malnutrition-modulated diabetes mellitus (MMDM), which was previously referred to as protein-deficient diabetes mellitus (PDDM) in the 1985 WHO classification. Insulin-dependent diabetes mellitus (IDDM) is a polygenic disorder with an autoimmune basis for disease development. In addition to HLA, a second susceptibility locus for IDDM has been identified to lie in the major histocompatibility class III region. Both IDDM and MMDM in eastern Indians are associated with DR3-DQ2 but not DR4-DQ8. The presence of autoantibodies to IDDM autoantigens in clinical MMDM either identifies the slow-onset form of IDDM or suggests autoimmunity different from that in IDDM. Our study demonstrates that the presence of GAD65 antibody and DR3-DQ2 positivity in MMDM patients identifies the underlying autoimmune mechanism in the etiology in eastern India. In autoantibody-negative MMDM patients an association with DR7-DQ2 is identified. The date obtained also indicate the possibility that MMDM can coexist with IDDM in these patients and that malnutrition could be one of the reasons for the slower onset in IDDM-prone individuals. The association of DR7-DQ2 suggests that there is a different immunogenetic background to MMDM than to IDDM. MICA is located in the MHC class I region and is expressed by monocytes, keratinocytes, and endothelial cells. Sequence determination of MICA gene identifies trinucleotide repeat (GCT) microsatellite polymorphism in exon 5. Five alleles with 4, 5, 6, and 9 repetitions of GCT or 5 repetitions of GCT with 1 additional nucleotide insertion (GGCT) are identified. The alleles are A4, A5, A5.1, A6, and A9. We studied the association of MICA alleles with IDDM (n = 52) and MMDM (n = 41) patients and healthy controls (n = 73) from Cuttack, eastern India. MICA was typed by PCR amplification, and fragment sizes were determined in an ABI prism DNA sequencer. Allele 9 of MICA is positively and allele 4 negatively associated with MMDM patients compared to controls. Allele 5 is positively associated with IDDM (OR 2.64, P < 0.05) when compared to controls. Our findings suggest that MMDM is immunogenetically different from IDDM in eastern India and that MIC-A is important in the pathogenesis of MMDM patients from Cuttack in eastern India.