This chapter examines collaboration in regenerative medicine research in Japan as the configurations of clusters', or formal and informal social ties and groupings of different actors. The new millennium was an important turning point for Japanese science and technology policy. The Millennium Projects were large-scale government research initiatives focusing on modern society information, ageing and environment. The chapter explains regenerative medicine research in Japan shows, the value of life science research is increasingly tied to its clinical relevance', and patient participation is becoming a major resource for one's legitimacy. Yamanaka's creation of human induced pluripotent stem (iPS) cells provided the government an opportunity to re-configure the cluster and justify its commitment after its unsuccessful attempts of the Millennium Genome Projects and the Project for Realization of Regenerative Medicine. The chapter demonstrates a field of science is being shaped not only by the researchers' attempt to draw its boundaries but also by the government's attempts to justify their policy decisions.