Bisphosphonates are carbon-substituted pyrophosphate (PCP) analogues that exhibit high affinity to hydroxylapatite and inhibit bone resorption after their administration. They are widely used as the first-choice drug for the treatment and prevention of bone diseases, including Paget's disease, hypercalcemia of malignancy, and osteoporosis. However, the oral bioavailability of bisphosphonates is quite low (1-2%). In addition, the oral administration of bisphosphonates has been associated with mucosal damage, including gastritis, gastric ulcer, and erosive esophagitis. Therefore, it is highly desirable to develop new delivery systems that improve their bioavailability and safety. In this review, recent challenges in the developments of novel delivery system of bisphosphonates are summarized. Then, future developments of delivery system of bisphosphonates are also discussed in order to improve their therapeutic efficacy and safety in the treatment of bone diseases.