The first generation of genetically modified plants suitable for agriculture was largely produced using antibiotic resistance markers (ARMs) for the preparation of plant transformation vectors or for the plant transformation process itself.  In some instances, the ARM gene remains in the finished commercial plant product. Theoretical concerns regarding the risks posed by such markers have resulted in a demand for the production of commercial plants free of ARMs. This, in turn, has resulted in the development of technologies which avoid the use of ARMs or which allow for the efficient excision of such markers following the initial transformation process, but in advance of the selection of commercial plant lines. We review the current status of ARM safety information relevant to existing genetically modified crops as well as reviewing in some detail the available alternatives to ARM use, the utility of these technologies for commercial production, and the issues that might pertain to the use of these alternative technologies for the production of commercial genetically modified crops. Many of the alternative techniques have the potential to be commercially viable, and one or more will necessarily be used for the future production of genetically modified plants free of ARMs. Nonetheless, existing ARM-containing products will remain in the market for the foreseeable future, and the safety of these products therefore remains a relevant issue. Further, the ease of use, cost, availability, safety profile, regulatory status, and utility of alternative techniques should be kept in proper perspective relative to the long history of safe use of ARMs in plant biotechnology.