The eotaxin gene family (eotaxin, eotaxin-2, and eotaxin-3) has been implicated in the recruitment of eosinophils, basophiles and Th2 lymphocytes that is a central aspect of allergic diseases. We previously suggested that Eo2+179T>C and Eo2+275C>T of the eotaxin-2, and Eo3+2497T>G of the eotaxin-3 were significantly associated with susceptibility to asthma. To precisely determine whether these single nucleotide polymorphisms (SNPs) are associated with susceptibility to autoimmune disease such as rheumatoid arthritis (RA) in Koreans, we analyzed the genotype and allele frequencies for four SNPs (Eo2+179T>C, Eo2+275C>T, Eo2+304A>C, and Eo2+1272A>G) of the eotaxin-2, and three SNPs (Eo3+77C>T, Eo3+1577G>A, and Eo3+2497T>G) of the eotaxin-3 by single-base extension method. Although the genotype and allele frequencies of the eotaxin-2 SNPs gene between patients with RA and controls were not significantly different, the genotype and allele frequencies of the eotaxin-3SNPs between them were significantly associated. The genotype frequencies of Eo3+1577G>A and Eo3+2497T>G in patients with RA were significantly different from those in the controls (p = 0.0001 and p < 0.0001, respectively). Our results strongly suggest that the polymorphisms of eotaxin-3 might be associated with susceptibility to RA.