Metabolic bone disease is a frequent complication of Crohn’s disease (CD) with the pathogenesis of reduced bone mass in CD reported to include body weight, disease severity, disease treatments and surgery, physical activity and nutritional status. To date, there have been no studies to examine the prevalence of osteopenia and osteoporosis in an Australian CD population. Similarly, the roles of disease state and treatment, lifestyle factors and the role of body composition in the development of bone loss in CD have not been examined in an Australian CD cohort to date. This thesis has sought, for the first time, to determine the prevalence and severity of bone loss in an Australian CD population and to examine the relationship between various clinical, genetic, lifestyle and treatment variables. The role of body composition in bone loss was assessed by close examination of the muscle-bone relationship by dual-energy X-ray absorptiometry (DXA) and the local muscle-bone unit by peripheral quantitative computed tomography (pQCT) so that informed targeted treatment strategies may be implemented. Study 1 assessed the prevalence of bone loss and both molecular and clinical risk factors for bone loss in a large Crohn’s disease population. Bone mineral density (BMD) data were combined with clinical information and correlated with single nucleotide polymorphisms within the TNF-α, interleukin-10, and NOD2/CARD15 genes. Study 2 examined the independent effects of body composition and muscle strength on regional and whole body BMD in a cohort of CD patients to determine their relative importance to bone strength in this population. Study 3 used pQCT for the first time in a CD population to assess the functional muscle-bone unit in order to determine if the high prevalence of low bone mass reported in CD patients is mediated by altered body composition, in particular muscle mass and strength. Study 1 revealed 45% of CD patients had previously been diagnosed with osteopenia and 18% with osteoporosis. Both the TNF-α “GT” haplotype and the -857 “CC” genotype showed strong associations with bone mineral density overall (p=0.003 and p=0.002, respectively). Body mass index (p=0.01) and previous bowel resection in females (p=0.03) were predictive of a higher spine bone density, whilst body mass index (p=0.003) and the effect of years since first bowel resection (p=0.02) remained independent predictors of proximal femur bone mineral density. When bone mineral density was assessed in Study 2, the prevalence of osteopenia and osteoporosis was 32% and 17%, respectively, with osteopenia more common at the hip and osteoporosis more common at the spine. In multiple regression analyses, appendicular muscle mass was an independent predictor of whole body and regional BMD while lean mass was an independent predictor at the hip. Neither grip strength nor fat mass were independently associated with BMD. Of the components of body composition, muscle mass was strongly associated with regional and whole body bone mineral density. When the muscle-bone unit was assessed using pQCT in Study 3 to further examine this relationship, CD patients demonstrated lower tibial shaft mass, tibial shaft cortical cross-sectional area, and proximal tibia bone mineral density than similarly aged healthy controls. CD subjects also had significantly lower areal bone mineral density by DXA than controls at the total body (P=0.038) and hip (P=0.019). There were no significant differences between groups for any of the muscle-bone indices assessed, such as bone mineral content/muscle cross-sectional area and bone cross sectional area / muscle strength. Together, these studies have demonstrated a high prevalence of metabolic bone disease in an Australian CD population. We were able to identify a novel protective association between a TNF-α haplotype and bone mineral density and also confirmed the importance of body mass index and intestinal resection on bone loss in this population. Furthermore, these studies indicated that lean mass, and more specifically muscle mass, was a significant independent predictor of regional and whole body BMD. Consequently, maintaining or increasing muscle mass in this patient population may have a positive effect on BMD and prevent the development of osteopenia and osteoporosis. Although only modest differences were found between CD patients and controls for areal BMD by DXA and some bone parameters by pQCT, there were no differences in indices of the muscle-bone unit. These results suggest that bone strength is adequate for muscle size and strength in our sample of male CD patients with well-controlled disease, inferring that no specific intervention is required to correct expected deficiencies in this relationship. Instead, an exercise training program introduced to this patient cohort should aim to maintain or increase bone mass through weight-bearing exercises as well as encourage the maintenance or increase in muscle mass.