The aim of this study was to investigate the correlation between single nucleotide polymorphisms (SNPs) of the forkhead box J3 (FOXJ3) gene and rheumatoid arthritis (RA). For the association studies, 307 patients with RA and 476 control patients without RA were recruited. Eleven SNPs (rs2282404, rs2455084, rs1393009, rs7539485, rs4660616, rs510157, rs343386, rs12732892, rs343389, rs343376 and rs585320) were genotyped using direct sequencing and the resulting data were analyzed using the SNPStats, Haploview and Helixtree programs. Seven SNPs (rs2455084, rs1393009, rs7539485, rs4660616, rs510157, rs343386 and rs343389) were associated with RA in three alternative models (log‑additive, dominant and recessive models; P<0.05). A strong linkage disequilibrium block, including all 11 SNPs, was constructed using the Gabriel method. Two haplotypes, TCCTTGTCTTT and TCTTCTGTCAC, were significantly associated with RA (P<0.05). In clinical characteristic analysis, the SNP rs585320 was also associated with the anti‑cyclic citrullinated peptide. These results suggest that FOXJ3 may be associated with the development of RA.