Protein-based therapeutic agents intended for bone diseases should ideally exhibit a high affinity to bone tissue, so that their systemic administration will result in specific delivery to bone with minimal distribution to extra-skeletal sites. This was shown possible in the authors' lab by modifying a desired protein with bisphosphonates (BPs) that exhibit an exceptionally high affinity to the bone-mineral hydroxyapatite. In this review, we explore the potential applications of that concept by summarizing the bone diseases and candidate proteins that will benefit from the proposed bone delivery approach. A selective synopsis of BP synthesis is presented to highlight the synthesis of functional BPs suitable for covalent attachment to proteins. Finally, we present a summary of recent research results from the authors' laboratory emphasizing factors influencing bone affinity of the conjugates. We conclude with future research avenues that are considered critical for clinical entry of the BP-targeted therapeutic agents.