Over the last decade vitamin D (Vit D) has been the focus of considerable interest as a potential immunomodulator in a variety of conditions including autoimmune disease. Its influence in juvenile idiopathic arthritis (JIA) however is unclear. We therefore wished to clarify a possible link with the currently available evidence. A systematic literature review was undertaken using Embase, Cochrane and Medline for manuscripts up to May 2011. Search results were then assessed by two independent reviewers and relevant articles were further screened by full text review. Only those specifically reporting Vit D levels or its supplementation in JIA (ages between 0 and 18 years) were selected. Meta-analysis was performed where possible with those papers reporting similar data and analysis techniques. In total, 19 papers (n = 745) were included in the review. Fourteen papers quoted 25(OH)D levels within their study groups with a mean of 24.56 ng/ml (range, 11.5-56.4 ng/ml) in a total of 529 children. Eleven papers quoted 1,25(OH)2D levels with a mean of 31.09 pg/ml (range 6.1-65.0 pg/mol) in a total of 518 children. Three studies reporting the prevalence of Vit D deficiency in their cohorts found that up to 82 % of children had insufficient levels. Five papers reported Vit D levels by JIA subtype and showed lower levels of both 25(OH)D [mean 15.35, range 8.5-24.5 ng/ml] and 1,25(OH)2D [ mean 22.89, range 5.6-50 pg/ml] in systemic JIA. Four papers reported Vit D supplementation in JIA however the treatment effect was unclear. At present no clear evidence exists to support a link between Vit D level and JIA. Furthermore, the role of Vit D supplementation in the management of JIA is lacking. Despite Vit D levels appearing to be lower in JIA, interpretation is problematic as no agreed definition of Vit D deficiency exists in this population. A need remains therefore to standardise Vit D levels in the paediatric population and in JIA.