Leflunomide is the drug used in the therapy for rheumatoid arthritis (RA). Previous studies indicated that the efficacy of the therapy with antirheumatic drugs is more effective in men than in women. Moreover, estrogens can decrease the anti-inflammatory action of leflunomide. Estrogens act through the estrogen receptors ESR1 and ESR2. In ESR1 and ESR2 genes, several polymorphisms have been detected. The aim of the present study was to examine the association between polymorphisms in the ESR1 and ESR2 genes and the response to treatment of RA patients with leflunomide. The study was carried out on 115 women, mean age 54.1 ± 11.0 years, diagnosed with RA and treated with leflunomide (20 mg daily). Our results indicated a better response to treatment in patients with ESR1 rs9340799 AA and rs2234693 TT genotypes after 12 months of therapy. In these patients, the improvement of erythrocyte sedimentation rate, patient's global assessment of disease activity on a 100 mm visual analog scale and disease activity score values was greater than in patients with other genotypes. The ESR1 rs9340799-rs2234693 A-T haplotype was associated with a better response to treatment, the G-C haplotype with a worse response and the A-C haplotype was neutral. There were no statistically significant associations of response to treatment with ESR2 gene rs4986938 and rs1256049 polymorphisms. The results of the present study suggest that ESR1 gene polymorphisms in females with RA may be associated with the response to treatment with leflunomide.