Background: Inflammatory bowel disease (IBD) is a chronic inflammatory immune-mediated condition that affects the gastrointestinal system and alters bone growth and bone mineral density (BMD). Here we aimed to study the prevalence and predictors of a low BMD in pediatric patients with IBD. Methods: This retrospective cross-sectional analytical study included pediatric patients with IBD in whom BMD was evaluated using dual energy X-ray absorptiometry of the total body and lumbar spine. Osteoporosis was defined as a BMD Z-score ≤-2, osteopenia as -2 to -1, and normal as >-1. Clinical and laboratory findings were compared between patients with and without osteoporosis. Results: Of the 48 patients, 30 (62.5%) were males, 35 (72.9%) had Crohn’s disease, and 13 (27.1%) had ulcerative colitis. The mean age at diagnosis was 9.9±2.8 years. The median age at the time of the BMD scans was 11.9 (interquartile range, 9.9–14.3) years. Total body BMD scans identified 13 (27.1%) and 16 (33.3%) patients with osteoporosis and osteopenia, respectively. Spinal BMD scans revealed that 17 (39.5%) and 14 (32.6%) patients had osteoporosis and osteopenia, respectively. A low body mass index (BMI) Z-score (p=0.038), ileocolonic disease location (p=0.008), and a low calcium level (p=0.008) were significant predictors of osteoporosis on the total body BMD scans. A low BMI Z-score (p=0.039), decreased hemoglobin level (p=0.018), low calcium level (p=0.033), and infliximab use (p=0.019) were significant predictors of osteoporosis on the spinal BMD scans. Conclusions This study showed a high prevalence of low BMD among pediatric patients with IBD. A low BMI, ileocolonic disease location, low hemoglobin and calcium levels, and infliximab use were significantly associated with osteoporosis.