Regulatory restrictions have increased in recent years on organisms produced using recombinant DNA and asexual gene transfer, a process commonly called genetic engineering or genetic modification. Regulatory agencies have raised special concerns and required additional scrutiny for perennial grasses and woody plants of interest for biofuels; these plants have incomplete domestication, invasive capabilities, and the ability to mate with wild or feral relatives. Regulations on these plants require extremely stringent containment through all phases of research and development, regardless of the source of the gene, the novelty of the trait, or the plants' anticipated economic or environmental benefits. We discuss the extent to which these requirements conflict with the realities of practical crop breeding, and prevent meaningful agronomic and environmental studies, thus hampering—and in most cases, precluding—the use of recombinant DNA breeding methods for perennial crop improvement. We propose regulatory reforms to better balance benefit and risk and remove unnecessary barriers to agronomic evaluations and environmental studies.