Selectable marker genes are widely used for the efficient transformation of crop plants. In most cases, selection is based on antibiotic or herbicide resistance. Due mainly to consumer concerns, a suite of strategies (site-specific recombination, homologous recombination, transposition and co-transformation) have been developed to eliminate the marker gene from the nuclear or chloroplast genome after selection. Current efforts concentrate on systems where marker genes are eliminated efficiently soon after transformation. Alternatively, transgenic plants are produced by the use of marker genes that do not rely on antibiotic or herbicide resistance but instead promote regeneration after transformation. Here, the merits and shortcomings of different approaches and possible directions for their future development are discussed.