Analysis of the NFKB1 rs28362491 polymorphic locus showed that in JIA patients with the insufficient response to methotrexate the NFKB1 rs28362491*DD genotype was significantly more common, and the NFKB1 rs28362491*ID genotype was significantly less common, than in those with the sufficient response (*DD: 28.03% vs. 12.50%, P = 0.010, pcor = 0.011, OR = 2.726, 95% CI 1.306–5.568; *ID: 38.64% vs. 62.50%, P = 0.001, pcor = 0.0008, OR = 0.378, 95% CI 0.213–0.675, respectively). Here, NFKB1 is linked to juvenile idiopathic arthritis.