The family of T-cell immunoglobulin domain and mucin domain (TIM) proteins is identified to be expressed on T cells. A member of TIM family, TIM-3 is selectively expressed on the surface of differentiated Th1 cells. TIM-3 might have an important role in the induction of autoimmune diseases by regulating macrophage activation and interacts with TIM-3 ligand to regulate Th1 responses. In the present study, we analyzed the association of the genotype and allele frequencies between rheumatoid arthritis (RA) patients and the controls without RA using large samples size at the -1516G>T, -574T>G and 4259G>T polymorphic sites of human Tim-3 gene. We further investigated the relationships between the genotypes of each single nucleotide polymorphisms (SNPs) and C-reactive protein (CRP) or rheumatoid factor (RF) levels in RA patients. The genotype and allele frequencies of the -574T>G (P = 0.001 and 0.001, respectively) as well as the 4259G>T (P = 0.001 ands 0.003, respectively) between RA patients and non-RA controls were significantly different. These results strongly suggest that -574T>G and 4259G>T polymorphism of the Tim-3 might be associated with susceptibility to RA.