Inflammatory bowel disease (IBD) is associated with low bone mineral density (BMD). In this study, the association between disease severity and BMD in patients with IBD was evaluated. Associations between BMD and the Montreal classification, disease activity and drug therapy were also tested. A cross-sectional prevalence study with a comparison group was conducted. One hundred and twenty-eight patients were evaluated: 68 patients with ulcerative colitis (UC), and 60 with Crohn's disease (CD). The control group consisted of 67 healthy subjects. All patients and controls had BMD measured and in IBD patients, current medications, hospitalization, and disease location, extent and phenotype, according to the Montreal classification, were recorded. Multiple correspondence analysis was applied to evaluate categorical variables. In the CD group, most patients were diagnosed between 17-40 years of age. Ileocolonic and non-stricturing non-penetrating disease were the most frequent disease location and behavior, respectively. In UC patients, extensive colitis was the most frequent disease location. UC and CD patients were more likely to have osteopenia than controls (OR=14.93/OR=24.38, respectively). In the CD group, male patients, perianal disease, penetrating behavior and age at diagnosis >40 years were associated with low BMD. Taking azathioprine and infliximab also seemed to be associated with osteopenia. In the UC group, we observed an association between low BMD and male patients, left colitis, corticosteroid use and hospitalization. Disease activity was not associated with osteopenia or osteoporosis in CD and UC patients. Disease severity seems to be associated with osteopenia in IBD patients.