The T-cell immunoglobulin and mucin domain 3 (TIM-3) has been shown to be associated with susceptibility to rheumatoid arthritis (RA). In this study, we investigated the association of four single-nucleotide polymorphisms (SNPs) of the TIM-3 gene with RA susceptibility in Chinese Hui and Han groups. Using restriction fragment length or sequence-specific primer–polymerase chain reaction (PCR), patients with RA and nonarthritis control individuals from these two ethnicities were analysed for SNPs of −1541 C>T, −882 T>C, −574 T>G and +4259 G>T, in the TIM-3 gene. Our results demonstrated that the polymorphisms of +4259 G>T SNP of TIM-3 gene was associated with the RA susceptibility in both the Hui (P < 0.01) and Han populations (P < 0.05). However, the −1541 C>T and −574 T>G SNPs were distinctly associated with RA for the Hui and Han populations, respectively. In addition, haplotype analysis found no statistically differences in the distribution of nine detected haplotype frequency between patients with RA and controls in this study (P > 0.05). These findings suggest that polymorphism of +4259 G>T in TIM-3 gene may be one of the most important genetic factors associated with the RA susceptibility among different populations, and genetic variations of TIM-3 gene contribute to RA susceptibility among different populations.