Objective. The response to and toxicity of methotrexate (MTX) are unpredictable in patients with juvenile idiopathic arthritis (JIA). Intracellular polyglutamation of MTX, assessed by measuring concentrations of MTX polyglutamates (MTXGlu), has been demonstrated to be a promising predictor of drug response. Therefore, this study was aimed at investigating the genetic predictors of MTXGlu variability and associations between MTXGlu and drug response in JIA.Methods. The study was designed as a singlecenter cross-sectional analysis of patients with JIA who were receiving stable doses of MTX at a tertiary care children's hospital. After informed consent was obtained from the 104 patients with JIA, blood was withdrawn during routine MTX-screening laboratory testing. Clinical data were collected by chart review. Genotyping for 34 single-nucleotide polymorphisms (SNPs) in 18 genes within the MTX metabolic pathway was performed. An ion-pair chromatographic procedure with mass spectrometric detection was used to measure MTXGlu 1-7 .Results. Analysis and genotyping of MTXGlu was completed in the 104 patients. K-means clustering resulted in 3 distinct patterns of MTX polyglutamation. Cluster 1 had low red blood cell (RBC) MTXGlu concentrations, cluster 2 had moderately high RBC MTXGlu 1 Ű 2 concentrations, and cluster 3 had high concentrations of MTXGlu, specifically MTXGlu 3-5 . SNPs in the purine and pyrimidine synthesis pathways, as well as the adenosine pathway, were significantly associated with cluster subtype. The cluster with high concentrations of MTXGlu 3-5 was associated with elevated liver enzyme levels on liver function tests (LFTs), and there were higher concentrations of MTXGlu 3-5 in children who reported gastrointestinal side effects and had abnormal findings on LFTs. No association was noted between MTXGlu and active arthritis.Conclusion. MTXGlu remains a potentially useful tool for determining outcomes in patients with JIA being treated with MTX. The genetic predictors of MTXGlu variability may also contribute to a better understanding of the intracellular biotransformation of MTX in these patients.The response to methotrexate (MTX) in patients with juvenile idiopathic arthritis (JIA) is variable, with no identified predictors of response or toxicity (1-3). The mechanism of action of the drug is complex and incompletely understood. However, over the past several decades, we have gained increasing knowledge regarding specific sites of MTX action within the cellular folate cycle. Due to its inhibitory effect on several target enzymes, we know that MTX disrupts the folate cycle, which results in decreased production of DNA precursors, disruption of methyl-dependent reactions, and accumulation of adenosine, the latter of which has antiinflammatory properties (4-6).