In light of larger public policy debates over intellectual property and climate change, this article considers patent practice, law, and policy in respect of biofuels. This debate has significant implications for public policy discussions in respect of energy independence, food security, and climate change. The first section of the paper provides a network analysis of patents in respect of biofuels across the three generations. It provides empirical research in respect of patent subject matter, ownership, and strategy in respect of biofuels. The second section provides a case study of significant patent litigation over biofuels. There is an examination of the biofuels patent litigation between the Danish company Novozymes, and Danisco and DuPont. The third section examines flexibilities in respect of patent law and clean technologies in the context of the case study of biofuels. In particular, it explores the debate over substantive doctrinal matters in respect of biofuels – such as patentable subject matter, technology transfer, patent pools, compulsory licensing, and disclosure requirements. The conclusion explores the relevance of the debate over patent law and biofuels to the larger public policy discussions over energy independence, food security, and climate change.