Investment in new energy technologies is inadequate relative to the timescale on which greenhouse emissions need to be reduced. This raises questions concerning the policy instruments intended to facilitate the spread of lower carbon energy supply technologies. This paper theorises the role of patent practices and relationships between firms of different size and power, drawing on what little evidence is available in relation to biofuels. We bring firm-level theory of value creation together with a critical perspective of selected innovation theory, to discuss the ways in which patents may be used such that the consequences are contrary to the public good. Considering the implications for clean energy technology transfer, particularly the case of biofuel technology, we conclude that while there is relatively little information on the ways in which patents may hinder clean energy technology transfer, there are certainly sufficient grounds for concern.