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The aim of this study was to determine whether children with celiac disease (CD) have deficits in spine (SP) and whole body (WB) bone mineral content (BMC) at time of diagnosis, and whether the deficits are related to altered growth and body composition. The secondary aim was to examine the effect of histological grade on BMC.A retrospective study of children who had undergone a dual energy x-ray absorptiometry scan at the time of diagnosis with CD between October 1, 2003, and June 15, 2006, were compared with a healthy reference sample of similar age and race from the same geographic region in the United States. SP and WB BMC were expressed as sex-specific z scores relative to age and relative to height to assess differences in the CD group versus controls. Pearson correlation, t tests, and analysis of variance were performed to determine predictors of BMC.Forty-four children (mean age 10.6 ± 3.4 years; 77% female, 96% white) with CD were evaluated and compared with 338 healthy children. Children with CD were shorter than children of similar age and sex. SP and WB BMC for age z scores were significantly lower in the CD group compared with controls. When adjusted for height, significant deficits in WB BMC persisted in patients with CD. Low SP and WB BMC correlated with advanced histological grade in CD. Low body mass index correlated with low WB BMC in CD.Newly diagnosed children with CD may benefit from screening for low bone mineral content. Patients with low body mass index and those with advanced histological damage (Marsh grade IIIc) particularly may be at risk for osteopenia.