Purpose: Low bone mineral density (BMD) is a complication in children with inflammatory bowel disease (IBD). There are limited data evaluating dual-energy x-ray absorptiometry (DXA) as a screening tool for low BMD in children with IBD. We performed a single site retrospective analysis of DXA use. Methods: Children aged 5–18 years with IBD diagnosed between 2013 to 2017 at the Royal Children’s Hospital, Australia, were included. Patient demographics, measures of disease activity, DXA scores, and factors related to BMD were collected. Results: Over a median follow up of 5.1 (4–6.4) years, 72/239 (30.1%) children underwent DXA, and 28/239 (11.7%) children had a second DXA. Our DXA practice differed to consensus guidelines regarding initial screening based on height and/or body mass index (BMI) z-score (8/17 [47.1%]), and repeat surveillance (13/42 [31.0%]). Children had a median lumbar spine (LS) z-score −0.80 (−1.65–0.075). Children with LS z-score≤−2.0 (n=14) had lower weight (6.57 [1.78–23.7] vs. 51.1 [26.5–68.7], p=0.0002) and height centiles (3.62 [1.17–17.1] vs.42 [16.9–67.1], p=0.0001), and higher faecal calprotectin (FCP) (3041 [1182–4192] vs. 585 [139–2419], p=0.009) compared to children with LS z-score>−2.0. No fractures were reported. Of 28 children who underwent a second DXA 1.6 (1.1–2.2) years following initial DXA, no significant change in z-scores occurred. Conclusion Children with IBD had low BMD. In addition to height centile and weight centile, FCP was associated with lower BMD, and should be considered in DXA screening guidelines. Greater clinician awareness of DXA consensus guidelines is required. Future prospective studies are required.