In recent decades, molecular hydrogen has been shown to have diverse biological effects. By the end of 2022, more than 2000 articles have been published in the field of hydrogen medicine, many of which are original studies. There is some preliminary evidence on the regenerative effect of molecular hydrogen when administered by inhalation or via drinking hydrogen-rich water. Here we propose a novel method of administering hydrogen via intraosseous route, which potentially enhances the tissue regenerative effect. The purpose of this review was to systematize ideas about the nature, characteristics, and mechanisms of the influence of molecular hydrogen on various types of cells, including stem cells, as well as to introduce the hypothesis of the potential advantages of intraosseous administration route. The molecular, cellular, tissue and systemic effects of hydrogen are also reviewed. The existing literature indicates that the molecular and cellular effects of hydrogen qualify it to be a potentially effective agent in regenerative medicine. Administration of molecular hydrogen via intraosseous route may serve as an optimal way to stimulate a bone marrow stem cell pool. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2024.