Microsatellite polymorphism in exon 5 of major histocompatibility complex class I chain related gene‐A (MIC‐A) has been implicated in the etiology of autoimmune diseases including type 1 diabetes (T1D) and celiac disease (CD). In this study on North Indian population, the MIC‐A5.1 allele, carrying a premature termination codon in transmembrane region, was observed with increased frequency in T1D (29.6%, odds ratio OR = 2.1, P = 0.00017) and CD patients (40.3%, OR = 3.37, P = 1.67E‐05) than in controls (16.7%). When the MIC‐A5.1 association was adjusted for linkage with human leukocyte antigen (HLA)‐DR3, the statistical significance of the association was abolished. This implies that the observed association of MIC‐A5.1 is due to its linkage disequilibrium (D′ = 0.94) with HLA‐B8‐DR3‐DQ2 haplotype and is secondary to the overall association with DR3 positive MHC haplotypes.