Background The pathogenesis of inflammatory bowel disease-associated osteopenia may be related to pathological rates of bone turnover; however, the literature shows mixed results.Aim To compare bone biomarkers in inflammatory bowel disease patients (Crohn's disease: n = 68, and ulcerative colitis: n = 32, separately) with age- and sex-matched healthy controls.Subjects Patients and controls were recruited from Cork University Hospital and Cork City area, respectively.Results Relative to that in their respective controls, Crohn's disease (n = 47) and ulcerative colitis (n = 26) patients (i.e. excluding supplement users) had significantly (P < 0.05-0.001) higher serum undercarboxylated osteocalcin (by 27% and 63%, respectively) and bone-specific alkaline phosphatase (by 15% and 21%, respectively) and urinary Type I collagen cross-linked N-telopeptides concentrations (by 87% and 112%, respectively). Relative to that in their respective controls, Crohn's disease and ulcerative colitis patients had significantly (P < 0.01) lower serum total osteocalcin (by 20% and 42%, respectively) and 25-hydroxyvitamin D (by 37% and 42%, respectively), while serum parathyroid hormone levels were similar. In the combined patient group (n = 100), undercarboxylated osteocalcin was positively associated with bone markers.Conclusions Both Crohn's disease and ulcerative colitis patients have altered bone turnover relative to that in healthy controls.