This paper presents the case study of the Estonian Genome Project (EGP) during its initial phase from 2001 to 2007. In these years, the EGP was an independent foundation established by the Estonian government and almost fully financed by foreign and local private venture capital. In essence, it was a public-private partnership in science, research and development. At the end of 2004, this governance structure broke down and private funding was pulled from the project. The paper discusses what went wrong with the EGP and what the main policy lessons are, namely that particularly developing and transition countries like Estonia with low administrative and policy implementation capacity should approach public-private partnerships in high-tech research and development with high caution as conflicts of interests and loss of accountability seem likely; this is particularly the case in biotechnology because of the high scientific and business uncertainty characteristic of the field.