Biosafety research on transgenic plants has become an important issue in ecological risk assessment. We summarize and assess the current status and future prospects of different approaches related to gene flow and its consequences. Firstly, we explain three appropriate components of biosafety research that include (a) characteristics of the target plant species and its crossable relatives, (b) phenotypic characteristics of the transgenic plant, and (c) the range of scientific questions addressed in the study. Secondly, we identify five different types of biosafety research based on studies without the use of genetically modified plants (GMPs) and the scientific methods used for examining GMPs. We did not expect that any one of the recent studies would be able to address all the appropriate components we suggested, but we point out the strengths of representative studies as well as their weaknesses. Finally, we give an outlook on the future of biosafety research in the post-commercialization era. Gene flow alone should be not regarded as an adverse environmental effect of transgenic plants. Because biosafety research is a time- and resource-intensive process, we will have to concentrate on causal-analytic monitoring with adequate baseline controls.