Introduction. The most widely accepted criteria to define an improvement in patient disease course in response to a therapeutic intervention are the American College of Rheumatology Pediatric response criteria developed in 1997. The genetic mutations in MTHFR gene are as well considered a background for improvement outcome difficulties. Aim of study. To assess the relationship between MTHFR gene mutations in JIA patients using methotrexate and the ACR Pedi 30% Index. Material and methods. An observational case-control study involved 68 patients using methotrexate for JIA treatment. The genetic polymorphism was tested and the appreciation of improvement was assessed after 24 weeks from treatment onset. Results. There has been examined 68 children, in whom the genetic testing revealed 23 (33,8%) cases of MTHFR combined C677T/A1298C (9 (39,1%)) and T677T (14 (60,9%)), and 45 (66,2%) cases of no mutations samples. The gender distribution was 37 (54,4%) girls and 31 (45,6%) boys with a mean age of 133,8 months CI 95% [0,81-0,97]. From the sample in which genetic polymorphism was found, only 2 (8,7%) children achieved low activity or disease remission, compared to 24 (53,3%) children from the mutation free sample, according to ACR Pedi 30% (χ²=12,842, p=0,0001). Conclusion. There has been determined a significant relationship between the MTHFR genetic background and the methotrexate response assessment over ACR Pedi 30% Index use in children with JIA.