Genes conferring resistance to antibiotics have been widely used as markers for the selection of transformed cells in the development of genetically modified (GM) plants. Their presence in GM plants released in the environment or used as food or feed has raised concerns over the past years regarding possible risks for human health and the environment. Although these concerns have not been supported so far by scientific evidence, the implementation of selection approaches avoiding the presence of antibiotic resistance marker genes (ARMGs) in the final GM plant is increasingly considered by GM plant developers, not only to alleviate the above-mentioned concerns, but also to circumvent technical limitations associated with the use of ARMGs. In the current paper, we present the results of a three-step analysis of selectable markers and reporter genes as well as methods aiming at developing marker-free GM plants. First, based on a comprehensive review of the scientific literature, technical developments in this domain are presented. Second, a state-of-the-art of the current use of selection approaches is provided based on publicly available information on GM plants tested in the field or authorized for commercialization. Third, in order to get more insight in the underlying practical, scientific and/or regulatory arguments supporting the choice of selection approaches, we present the results of a survey directed at relevant developers and users of GM plants. The applicability, efficiency, operational access and biosafety of the various selection approaches is discussed and considered in light of their current use, and in perspective to the long history of use of ARMGs in plant biotechnology.