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Children with celiac disease (CD) are susceptible to reduced bone mineral density (BMD). Our target is to assess the severity of vitamin D deficiency in CD children on a gluten-free diet (GFD), and to evaluate the effectiveness of adding an innovative GF meal, on the clinical and bone biochemical indices of CD patients. 50 CD children who were diagnosed and followed up at Pediatric gastroenterology clinic, Specialized pediatric hospital, Cairo University; by serology and biopsy of the duodenum were included in this prospective study. CD children were on GFD for at least one year. As a control group, 40 healthy children were enrolled. Thorough clinical examination, anthropometric assessment, a complete history and 24 hours dietary recall were done for all the participants in this work. We introduced our innovative GF meal to CD patients twice/day, for 3 consecutive months. Venous blood samples were withdrawn from patients at the study beginning and after 3 months for detection of serum vitamin D, calcium, phosphorous and alkaline phosphatase levels. The anthropometric measurements, serum vitamin D, and calcium were markedly decreased in CD children than that of controls. In CD patients, a significant increase in anthropometric parameters, vitamin D and calcium were found. While there was a significant decline of serum alkaline phosphatase, and a slight decrease in serum phosphorus at the study end. The innovative gluten-free prepared meal confirmed to be of high nutritional value in the management of vitamin D deficiency and improvement of bone indices in CD patient.