When a segment of a specific viral genome is expressed in a transgenic plant, the plant is often resistant to that virus. This promising method of deriving virus resistance appears also to provide an opportunity for RNA recombination. Several reports confirm that the viral transgenic transcript is available to a challenging virus for recombination. Using cowpea chlorotic mottle virus as a model, modifications of the transgene significantly reduced the recovery of viable recombinants from transgenic plants. Several recommendations are made for reducing the involvement of the transgene in RNA recombination events.