In the past few years many initial and subsequent clinical studies have demonstrated that hydrogen can act as an important physiological regulatory factor to cells and organs on the antioxidant, anti-inflammatory, anti-apoptotic and other protective effects. So far several delivery methods applied in these studies have proved to be available and convenient, including inhalation, drinking hydrogen-dissolved water and injection with hydrogen-saturated saline. This study reviews recent studies on the protectiveness of hydrogen and discusses the possible mechanisms including antioxidant ability as a gaseous signaling molecule, anti-cancer capability and others. It also tries to reveal whether endogenous hydrogen has an important role in the protective system. Nevertheless, there are still many remaining questions in the domain of hydrogen medicine and much work needs to be carried out in the future.