Biomarkers are being increasingly used in basic and clinical research of HIV disease as well as clinical management of infected individuals. Bone metabolism can be assessed by measurement of bone turnover markers, molecules released during bone formation and removal of old bone (resorption). In HIV-infected adults, there is a higher prevalence of low bone mineral density and fractures compared to the general population. This review discusses the findings regarding bone turnover markers in HIV-uninfected and -infected populations and their potential role in assessing fracture risk and predicting bone loss. Studies in postmenopausal women and elderly men show that increased bone turnover markers levels are associated with bone loss, and high levels of resorption markers may predict fractures independently of bone mineral density. Several HIV-related factors, including HIV infection and inflammation, have been found to affect the balance between bone formation and resorption. Some clinical studies found increased levels of bone turnover markers in HIV-infected adults compared to uninfected controls. Furthermore, bone turnover marker levels increased following initiation or switch to different antiretroviral agents in recent randomized trials. The clinical value of bone turnover markers is currently limited due to different sources of variability and limited data from studies in HIV-infected populations. Further research is needed to explore the potential value of bone turnover markers as additional measurements to bone mineral density in fracture risk assessment and monitoring treatment-induced bone effects in HIV-infected patients.