The 2013 Santa Fe Bone Symposium included plenary sessions on new developments in the fields of osteoporosis and metabolic bone disease, oral presentations of abstracts, and faculty panel discussions of common clinical conundrums: scenarios of perplexing circumstances where treatment decisions are not clearly defined by current medical evidence and clinical practice guidelines. Controversial issues in the care of osteoporosis were reviewed and discussed by faculty and participants. This is a review of the proceedings of the Santa Fe Bone Symposium, constituting in its entirety an update of advances in the understanding of selected bone disease topics of interest and the implications for managing patients in clinical practice. Topics included the associations of diabetes and obesity with skeletal fragility, the complexities and pitfalls in assessing the benefits and potential adverse effects of nutrients for treatment of osteoporosis, uses of dual-energy X-ray absorptiometry beyond measurement of bone mineral density, challenges in the care of osteoporosis in the very elderly, new findings on the role of osteocytes in regulating bone remodeling, and current concepts on the use of bone turnover markers in managing patients with chronic kidney disease who are at high risk for fracture.