In transformation of crop plants, the transfer of antibiotic marker genes or vector sequences to the environment or gut microbes is increasingly viewed as posing an unacceptable risk. Inserting foreign genes into plastid DNA is one way of minimizing transgene escape; however, conventional methods still leave behind marker and vector sequences. In this issue, Day and Iamtham describe a procedure that uses homologous recombination to generate transplastomic tobacco plants free of these controversial sequences. In their plastid expression cassettes, reporter (uidA) and herbicide resistance (bar) coding regions flank the antibiotic resistance marker (aadA), and include direct repeats that mediate the antibiotic marker gene's excision through homologous recombination and plastid segregation. The first-generation plants were free of aadA, and subsequent crosses produced plants free of both aadA and bar genes (see p. 1172).