Purpose: Children with celiac disease (CD) are at an increased risk of low bone mineral density (BMD) owing to malabsorption of fat-soluble vitamins, inflammation, and malnutrition. This study aimed to determine the prevalence and risk factors for low BMD in Iranian children with CD. Methods: This prospective cohort study examined 149 Iranian children with CD between 2011 and 2018 at Zabol University of Medical Sciences. BMD was measured using dualenergy X-ray absorptiometry. Demographic, clinical, and laboratory data were collected from patients’ medical records. Logistic regression analysis was performed to identify the factors associated with low areal BMD (BMD-Z <−2) in the lumbar spine and femoral neck.Descriptive data were analyzed using the mean, standard deviation, and relative frequency.Data were analyzed using the chi-square test, t-test, and analysis of variance. Results: Of the 149 children with CD, 27.5% had osteoporosis. The mean body mass index (BMI) Z score was −1.28±1.2. Lower BMI was associated with a higher likelihood of BMD-Z (odds ratio 2.17; p≤0.05). Conclusion Overall, the findings of this study showed that there was no correlation among Marsh classification, presence of specific human leukocyte antigens, and low BMD in Iranian children with CD. BMI can be a predictor of bone density in children with CD and may be applied clinically in early screenings to evaluate the bone health status in these children.