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Background: Childhood-onset systemic lupus erythematosus (cSLE) is a lifelong autoimmune disorder. The vitamin D receptor (VDR) gene is a potential candidate gene for cSLE susceptibility. In this study, we aimed to investigate the FokI polymorphism in the VDR gene in Egyptian children and adolescents with SLE, to determine whether this polymorphism could be a genetic marker for cSLE susceptibility or disease activity and we also measured the serum level of 25-hydroxyvitamin D [25(OH) D] to assess its relation to such polymorphism. Methods: This was a case-control study, which included 300 patients with cSLE and 300 age, sex, and ethnicity-matched healthy controls. All participants were genotyped for the VDR gene FokI (rs2228570) polymorphism by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP), while the serum [25(OH) D] levels were measured by enzyme-linked immunosorbent assay (ELISA). Results: The VDR FokI FF genotype and F allele were overrepresented among cSLE patients compared with the controls, [odds ratio (OR¼2.7; 95% confidence interval (CI): 1.6-4.4 for the FF genotype; p¼0.000; and OR¼1.6; 95% CI: 1.27-2.05 for the F allele; p¼0.000, respectively]. We found a significant association between VDR FokI FF genotype with lupus nephritis (OR: 4.8; 95% CI: 2.2-10.6; p¼0.002); and high disease activity index score (p¼0.01). Conclusions: The FokI polymorphism in the VDR gene may contribute to susceptibility to SLE in Egyptian children and adolescents. Moreover, the FF genotype constituted a risk factor for the development of lupus nephritis and was associated with low serum [25(OH) D] levels as well as higher disease activity index score among studied patients with cSLE. [ABSTRACT FROM AUTHOR]