Objective To investigate the relationship between the single nucleotide polymorphism of aminoimidazole carbexamide ribonucleotide transformylase gene and the efficacy and toxicity of methotrexate treatment in rheumatoid arthritis. Methods Total of 359 patients with RA were divided into mono-therapy with MTX group, combination therapy with other DMARDs group and other DMARDs combination with no MTX treatment group. The clinical and laboratory measurements were evaluated before therapy and 12, 24 weeks after therapy. Efficacy (evaluated by ACR20) and side effects of the drugs were also assessed. Real-time fluorescent quantitative PCR was conducted to test ATIC 347C/G mutation in RA patients and 340 healthy controls. Results There was no statistical significant difference in 347 CC, CG, GG between RA patients and healthy controls. In the MTX mono-therapy group (n=107), 72% (n=77) there was no statistical significant difference in 347CC, CG, GG between patients with good response and patients without efficacy. 32.7%(n=35) of these patients experienced adverse drug reactions. The ATIC G allele carriers (22.4%) experienced a greater frequency of side effects than the CC carriers (OR=2.672, 95%CI, 1.27～5.59, P<0.05). In MTX combined with other DMARDs group (n=128) and other DMARDs combination without MTX group (n=90), the polymorphism in the ATIC gene was not associated with good clinical response and adverse events (P>0.05). Conclusion There is no statistical significant difference between RA and healthy controls in the ATIC347 gene. Polymorphism in the ATIC gene is not associated with clinical response to MTX treatment, but the ATIC347 G allele is associated with MTX toxicity. It maybe used to predict the adverse drug reactions of patients who take MTX.