Molecular hydrogen (H 2 ) was long regarded as non-functional in mammalian cells. We overturned the concept by demonstrating that H 2 exhibits antioxidant effects and protects cells against oxidative stress. Subsequently, it has been revealed that H 2 has multiple functions in addition to antioxidant effects, including antiinflammatory, anti-allergic functions, and as cell death and autophagy regulation. Additionally, H 2 stimulates energy metabolism. As H 2 does not readily react with most biomolecules without a catalyst, it is essential to identify the primary targets with which H 2 reacts or interacts directly. As a first event, H 2 may react directly with strong oxidants, such as hydroxyl radicals (•OH) in vivo. This review addresses the key issues related to this in vivo reaction. •OH may have a physiological role because it triggers a free radical chain reaction and may be involved in the regulation of Ca2+- or mitochondrial ATP-dependent K+-channeling. In the subsequent pathway, H 2 suppressed a free radical chain reaction, leading to decreases in lipid peroxide and its end products. Derived from the peroxides, 4-hydroxy-2-nonenal functions as a mediator that up-regulates multiple functional PGC-1α. As the other direct target in vitro and in vivo, H 2 intervenes in the free radical chain reaction to modify oxidized phospholipids, which may act as an antagonist of Ca2+-channels. The resulting suppression of Ca2+-signaling inactivates multiple functional NFAT and CREB transcription factors, which may explain H 2 multi-functionality. This review also addresses the involvement of NFAT in the beneficial role of H 2 in COVID-19, Alzheimer’s disease and advanced cancer. We discuss some unsolved issues of H 2 action on lipopolysaccharide signaling, MAPK and NF-κB pathways and the Nrf2 paradox. Finally, as a novel idea for the direct targeting of H2, this review introduces the possibility that H 2 causes structural changes in proteins via hydrate water changes.