Since the first publication on biological effects of bisphosphonates appeared in 1969, during the past forty years, the mechanism of bisphosphonates has become increasingly well established, including the inhibition of adenosine triphosphate pathway and mevalonate pathway, as well as reduction of bone remodeling that leads to increased bone mineral density and reduced fracture rates. However, in addition to gastrointestinal irritation and acute side effects, long term use of bisphosphonates could impair the bone repair function, accumulates microdamages, and increase the risk of atypical fractures and osteonecrosis of the jaw. These serious side effects have raised concerns about the safety of bisphosphonates. With the hope to benefit clinical practice, the article reviews current studies about the biochemical and pharmacological properties of bisphosphonates, effects on bone metabolism, therapeutic efficacy of osteoporosis treatment, and related safety issues.