To investigate whether genetic variations of MICA are associated with susceptibility to rheumatoid arthritis (RA), the (GCT)n microsatellite polymorphism of the transmembrane domain was analyzed in 144 Korean patients with RA and in 297 unrelated healthy controls. The allele frequency of MICA*A9 significantly decreased in RA patients compared with controls (9.0% vs. 15.3%, odds ratio [OR] = 0.55, p = 0.0098, p(c) = 0.049), whereas the frequency of the MICA*A4 and MICA*A5.1 alleles tended to increase in RA patients (21.2% vs. 14.8%, OR = 1.55, p = 0.018, p(c) > 0.05; 20.5% vs. 15.0%, OR = 1.46, p = 0.0403, p(c) > 0.05). By subgroup analysis, the MICA*A4 allele significantly increased in seropositive RA patients versus controls (23.0% vs. 14.8%, OR = 1.69, p = 0.0082, p(c) = 0.041). HLA-DRB1*0405 was strongly associated with RA (p(c) = 0.0000008), and strong linkage disequilibrium was observed between HLA-DRB1*0405 and MICA*A4 alleles in controls (p(c) = 0.000004) as well as in RA patients (p(c) = 0.0012). In Korean patients, HLA-DRB1*0405 was primarily associated with RA and the weak association of RA with MICA*A4 was secondary to that with HLA-DRB1*0405. Additionally, MICA*A9 might have a weak protective effect on the susceptibility to RA in Koreans.