It is generally assumed that RNA recombination is one of the major driving forces in the evolution of plant viruses. This process leads to rearrangements of viral genomes and plays an important role in adaptation, genome repair and genetic variability of RNA viruses. It has been observed that viruses could recombine not only with each other, but also with mRNA of transgenic plants expressing viral genes. This observation has given rise to new concerns about creating virus-resistant transgenic plants, because the recombination could generate the viruses with new properties that were different from the parental strains. In this article, we present the current state of knowledge about recombination between transgens and challenging virus, we discuss what may happen in a field during interaction between the virus and the transgenic plant, and we propose strategies that allow to control the virus-transgene crossovers.