The use of transgenic tools for the improvement of plant feedstocks will be required to realize the full economic and environmental benefits of cellulosic and other biofuels, particularly from perennial plants. Traits that are targets for improvement of biofuels crops include herbicide resistance, pest, drought, cold and salt tolerance, nutrient use efficiency, altered cell wall composition and improved processing and end-use characteristics. However, controlling gene flow is a major issue and there is no regulatory experience with perennial plants as dedicated biofuels feedstocks. Bioconfinement of transgenes is thus an obvious regulatory and biosafety objective to the release and commercialization of transgenic bioenergy feedstocks. In this article, we review bioconfinement strategies that target pollen or seeds that can be applied to perennial plants used as biofuels. These include male sterility, integration of transgenes into plastid genomes, removal of transgenes in pollen and seeds, transgene expression in vegetative organs for harvest before appearance of reproductive structures or gene use restriction technologies.