The current study aims to evaluate bone mineral density (BMD) in patients with celiac disease who were referred to the celiac clinic of Shahid Rahimi Hospital in Khorramabad, Iran, in 2020. Extraintestinal presentations of celiac disease are widespread and, if neglected, can be devastating. Osteoporosis, one of the extraintestinal manifestations of celiac disease, often remains undiagnosed until advanced stages and can impose a significant burden on patients with celiac and health systems. Nonetheless, the prevalence and characteristics of osteoporosis in celiac disease are unknown in Iran. This was a cross-sectional study at the celiac clinic of Shahid Rahimi Hospital in Khorramabad, Iran. Participants were 48 patients under 18 years diagnosed with Marsh II and Marsh III stages of celiac disease (who need to be on a gluten-free diet) at the pediatrics celiac clinic in 2020. All patients were recruited, completed a questionnaire, and had their blood biochemical parameters analyzed. Then their bone mineral density (BMD) was measured through dual-energy x-ray absorptiometry at the Asia Imaging Center in Khorramabad under the supervision of a radiologist and pediatric rheumatologist. The mean age of the children was 9.96±3.17 years. The minimum and maximum ages of the participants were 4 and 17 years, respectively. Of all 48 children who were included (48), 34 (70.8%) were female, and 14 (29.2%) were male. In the femoral region bone densitometry, 35.4% were normal, 41.7% had lower limit normal, and 22.9% had low bone density. In the lumbar region, 39.6% were normal, 25% were Lower limit normal, and 35.4% had low bone density. No significant correlation was found between age, sex, place of residence, Marsh stage, gluten-free diet, and bone densitometry in both lumbar and femoral regions. Nonetheless, we detected a statistically significant relationship between bone density in the lumbar region and two HLA types, namely HLA DQ8 and HLA DQ2/8 (P=0.016). The results of the current study provided further evidence that all children with advanced celiac disease should be screened for metabolic bone diseases. Besides those in Marsh II and Marsh III, patients in Marsh I stage should also be investigated for low bone mineral density.