Chronic inflammation and malabsorption in gastrointestinal disease can cause bone metabolism alterations and bone mineral loss in children and adults. Gastrointestinal disease is often forgotten as a cause of osteoporosis, osteopenia, or osteomalacia. The etiology of pathologic bone alterations in gastrointestinal disease is multifactorial. Bone alterations were thought to result simply from intestinal malabsorption, but a more complex interaction between cytokines and local/systemic factors influencing bone formation and resorption is envisaged. This review provides an updated discussion on bone alterations in patients with malabsorption due to celiac disease or inflammatory bowel disease.