Background. Major histocompatibility complex class I chain-related gene A (MICA) is a ligand for the activating NKG2D receptor expressed on natural killer (NK) cells. We aimed to assess the association of MICA polymorphism with autoimmune thyroid disease (AITD) in Korean children. Methods. Eighty-one patients with AITD were recruited. We analyzed MICA polymorphisms by PCR-SSP and compared the results with those of 70 healthy controls. Results. In AITD, the allele frequencies of MICA∗010 (OR = 2.21; 95% CI, 1.30-3.76, P < 0.003, P(c) < 0.042) were higher than those of controls. Patients who did not have thyroid-associated ophthalmopathy showed higher frequencies of MICA∗010 (OR = 2.99; 95% CI, 1.47-6.08, P < 0.003, P(c) < 0.042) and lower frequencies of MICA∗008 (OR = 0.08; 95% CI, 0.01-0.62, P < 0.001, P(c) < 0.014) compared to those of controls. HLA-B∗46, which shows the strongest association with AITD compared with other HLA alleles, showed the strongest linkage disequilibrium with MICA∗010. Analyses of the associations between MICA∗010 and HLA-B∗46 with AITD suggest an association of the MICA allele with AITD. Conclusions. Our results suggest that innate immunity might contribute to the pathogenesis of AITD.