This study aimed to compare the bone mineral density (BMD) of patients with ulcerative colitis (UC) and Crohn's disease (CD) in order to determine the possible risk factors for bone loss. A total of 142 patients with UC (n = 88) and CD (n = 54) participated in the study. They were assessed for gender, body mass index (BMI), disease duration and activity, intestinal site of involvement, history of bowel resection, use of steroids, and extra-intestinal findings and complications. The BMD was measured by dual-energy X-ray absorptiometry. There were no differences in BMD between UC and CD patients. In UC patients, BMI showed a significant positive correlation with BMD. Femoral neck Z scores were lower in patients with extra-intestinal findings and complications. Steroid use, disease activity, disease localization, disease duration, bowel surgery and gender had no influence on BMD. Complications or extra-intestinal involvement were a significant predictor for BMD in both groups.