Patients on long-term parenteral nutrition (PN) are at significantly increased risk for the development of metabolic bone disease (MBD); this condition is characterized by incomplete mineralization of osteoid with consequent disturbances ranging from osteopenia to severe bone disease with fractures. The aim of the study was: (1) to evaluate the prevalence of MBD, (2) to identify the PN- or intestinal failure (IF)-related factors and (3) to assess annual changes of bone mineral status. Since September 2005 all patients affected by IF and treated with PN started a BMD evaluation program using dual-energy X-ray absorptiometry (DXA). Twenty-four IF patients were included [15 with short bowel syndrome (SBS), 5 with severe protracted diarrhea and 4 with chronic intestinal pseudostruction]. The bone mineral density (BMD) Z-score was significantly lower in patients than in the control group. In our series SBS patients showed a BMD Z-score significantly higher in comparison with the medical causes of IF. No significant correlations were found between bone mineral status and PN duration and nutrient intake. Nine IF patients were submitted to a second DXA evaluation after 1 year from the baseline. All bone mineral variables were significantly increased at the second DXA evaluation. The high prevalence of MBD in IF patients undergoing long-term treatment with PN requires that these patients undergo careful and periodic monitoring of their bone mineral status; patients with congenital gut dysfunctions, such as epithelium defects and motility anomalies, are at major risk of developing this complication, probably due to the association with extra-intestinal causes of bone loss.