This article follows the transformation of discourses and practices concerning organ transplantation in Japan, as well as considers the effect of comparison in dealing with the recent transformations of this medicine. Since the first enactment of the Japanese Organ Transplantation Law in 1997, public interest has shifted from cultural meanings of medicine to governance by numbers. When the Organ Transplantation Law was revised in June 2009, people seemed to be concerned about the number of donations more than ever and tended to pay less attention to the scientific controversy that had surrounded the redefinition of death in Japan since the 1960s. It is fair to say that the discourse about the shortage of organs occupies an increasingly important place in recent debates and serves as a mode of justifying brain death and organ transplantation. There is therefore an urgent need to analyze how the controversy between science and culture has been overcome during these twelve years. What kinds of criteria have been newly employed to justify brain death and promotion of donation? It is now impossible to ignore new kinds of biopolitics if one wants to understand how the human condition has been reconceptualized in recent medical and legal practice. By focusing on the social meaning of the shortage of organs and on the changing arguments justifying organ transplantation, I discuss the biopolitical conjuncture between economies and bodies and argue that, on the emerging biopolitical scene, organ donation and brain death are interpreted through economic practices.