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Successful collaborations between university and industry (U–I) promise numerous mutual benefits. In order to realize these benefits, both parties need effective governance mechanisms to overcome organizational and cultural barriers. Until 2004 in Japan, national universities were government organizations, and as such, they were prevented from actively pursuing collaborations with industry. Under this restriction, U–I collaborations were established through informal interpersonal networks. Joint R&D projects were inherently small and seldom likely to generate concrete results for industry. After a series of institutional and organizational reforms by the Japanese government, universities and industries adopted a new strategic approach in the early 2000s to form inter-organizational alliances. Based on the case of the Tokyo Institute of Technology, this paper analyzes how the inter-organizational alliances are managed and investigates their impact on joint R&D projects, in comparison with the traditional interpersonal networks. Additional research indicates that most national and private universities adopt management schemes similar to those presented in the case study. The findings suggest that inter-organizational U–I alliances, being equipped with contractual arrangements, organizational commitments, specialized coordination, and formal evaluation procedures, enable alliance partners to initiate more explorative research, to organize interdisciplinary projects with faculties in different research fields, and to establish larger-scale R&D projects.