Pairs of defective cauliflower mosaic virus genomes coinoculated in plants are rescued at high frequency by homologous, intergenomic recombination events. Defective genomes may be rescued by one of at least two general types of recombination mechanisms. One mechanism appears to operate on linear DNA molecules with complementary sticky ends. Recombination of this type can be explained by the formation of mixed dimers (or concatamers) which can be resolved into normal genomes by a single crossover event. Another type of recombination takes place among viral DNA molecules which do not have complementary sticky ends. Rescue of this type yields normal viral DNA molecules which can be resolved only by the equivalent of a double crossover or internal gene conversion event between pairs of infecting molecules. Co-infection of plants with pairs of defective genomes derived from different viral isolates results in the formation of hybrid viral genomes. Analysis of these hybrids reveals that recombination can take place at different sites in the viral genome.