This paper explores the effects of the change of organisational missions and R&D performance management systems on knowledge transfers within national innovation systems. Front the longitudinal and illustrative Case Study of a Korean Government research institute, the Electronics and Telecommunications Research Institute (ETRI), this paper shows that many technologies were transferred to large companies in the early days and the amount of knowledge transferred to small- and medium-sized companies increased during the 1990s when systematic performance evaluation systems developed. Recently, the commercialisation of the R&D results through spin-offs has become a key mechanism of knowledge transfer. In addition to traditional knowledge transfer, the mobility of researchers has contributed to knowledge transfer over national innovation systems. The researchers have moved not only to the private sector to commercialise R&D results, but also to academic institutes to develop human resources within the national innovation system. This paper suggests some policy implications on how the change of R&D management systems of government research institutes Could contribute to the development of national innovation systems,