BACKGROUND: A high prevalence of osteoporosis is found in patients with Crohn's disease. The pathogenesis of this condition seems to be multifactorial and its pathophysiology is still not completely understood. AIM: To elucidate the pathophysiology of osteopenia in quiescent Crohn's disease. METHODS: Bone turnover was studied in 26 patients (13 males and 13 females) with long-standing quiescent Crohn's disease and small bowel involvement. Bone mineral density was assessed by dual energy X-ray absorptiometry. Biochemical markers for bone formation (osteocalcin and bone-specific alkaline phosphatase) and for bone resorption (deoxypyridinoline and collagen type I C-terminal crosslinks) were measured. Urinary calcium excretion was determined. RESULTS: Markers for bone formation were significantly lower in patients than in controls (osteocalcin: P= 0.027, bone-specific alkaline phosphatase: P < 0.001), but both bone resorption markers were not significantly different. Urine calcium excretion was significantly decreased in patients (P=0.002) compared to controls. Bone mineral density of the lumbar spine was significantly and inversely correlated with bone-specific alkaline phosphatase and collagen type I C-terminal crosslinks. CONCLUSIONS: Bone turnover in long-standing Crohn's disease in clinical remission is characterized by suppressed bone formation and normal bone resorption. Urine calcium excretion is decreased. Hence, interventions and therapy should be directed towards the improvement of bone formation.