Background: Kashin-Beck disease (KBD) is a childhood-onset endemic osteoarthropathy in China. Nutrients including trace elements may play active roles in the development of KBD. Objective: This study aimed to estimate the nutrient intakes of children in endemic areas and to identify the imbalanced nutrients associated differentially expressed genes in the juvenile patients with KBD. Methods: In this cross-sectional study, a consecutive 3 day 24 h semi-quantitative dietary retrospect questionnaire was conducted to estimate the daily nutrient intakes of children using CDGSS 3.0 software. Gene profile analysis was employed to identify differentially expressed genes in peripheral blood mononuclear cells of children with KBD. GOC, CTD, KEGG, and REACTOME databases were used to establish the relationship between nutrients and nutrients-associated differentially expressed genes and pathways. Statistical analyses were accomplished by SPSS 18.0 software. Results: Daily Se intakes without supplementation of children were significantly lower in Se-supplemented (Se +) KBD areas (29.3 ∼ 29.6 mg/d) and non-endemic area (27.8 ± 7.9 mg/d) compared to non-Se-supplemented (Se-) KBD area (32.9 ± 7.9 mg/d, c2 = 20.24, P <.01). Children in Se+ KBD areas were suffering more serious insufficient intake of multiple nutrients, including vitamins-B2/-C/-E, Ca, Fe, Zn and I. Gene profile analysis combined with bioinformatics technique identified 34 nutrients associated differentially expressed genes and 10 significant pathways which are related to the pathological changes in juvenile KBD. Conclusions: Imbalance of dietary nutrients and nutrients-associated differentially expressed genes and pathways may play important roles in the development of juvenile KBD. © 2018 Elsevier GmbH