Associations of HLA-DR3/DQ2 with GAD65 and DR4 with IA-2 antibodies in insulin-dependent diabetes mellitus (IDDM) and DR3/DQ2 with GAD65 antibodies in latent autoimmune diabetes in adult (LADA) patients are known. The aim of the present study was to look for association of HLA DR and DQ with GAD65, IA2 and ICA12 antibodies in IDDM (n = 97), LADA (n = 32), and malnutrition-modulated diabetes mellitus (MMDM) (n = 22) patients from northern India. HLA genotyping was done by the PCR-SSO method. Antibodies to GAD65, IA-2, and ICA-12 were assayed by radioimmunoassay using (35)S-labeled recombinant human GAD65, IA2, and ICA12 using the in vitro transcription-translation method. We found DR3 (29% vs. 11%) and DQ2 (36% vs. 14%) were increased in GAD65 antibody-positive compared to GAD65 antibody-negative IDDM patients (P > 0.05). ICA 12 antibodies were increased in either DR3 or DR4 (84% vs. 69%) positives compared to non-DR3/DR4 IDDM patients (P > 0.05). However in LADA patients, ICA12 was increased in non-DR3/DR4 patients compared to DR3- or DR4-positive patients (P < 0.05). In conclusion, in LADA patients, ICA 12 is associated with non-DR3/DR4 patients. No association between HLA and autoantibodies was seen in MMDM patients.