This article elaborates on legal uncertainties in crop genetic improvement technologies within EU regulation on GMOs. Legal issues in plant breeding are explained, and specific challenges to the overall effectiveness of GMO regulation are exposed. The total of corroborations as to whether EU regulation on GMOs provides legal certainty concerning the application and exploration of plant breeding techniques is mostly negative. It appears that to warrant legal certainty, EU regulation on GMOs should respond to the needs of plant breeding in an efficient manner. In pursuit of desirable outcomes, law should be coherent and adequate to state-of-the-art technologies and to public perspectives on recent technological developments.