Extensive recombination events characterize higher-plant mitochondrial DNAs. Numerous recombination events resulted in the appearance of an unusual mitochondrial open reading frame, urf13-T, which encodes a 13 kDa polypeptide in the male-sterile T cytoplasm of maize. Maize lines with T cytoplasm are unusually susceptible to two fungal pathogens which produce host-selective toxins. Mutants derived from tissue culture expressing male fertility and toxin-insensitivity are characterized by truncation or deletion of urf13-T. These events result from a frameshift associated with a tandem 5 base pair repeat, placing a premature stop codon in frame, or from a recombination event, apparently limited to tissue culture, resulting in the deletion of urf13-T. Neither class of mutants produces the 13 kDa gene product. Repeated sequences that participate in recombination in sorghum appear to be randomly distributed among male-fertile or male-sterile cytoplasms. Processes involved in the evolution of mitochondrial DNAs in higher plants therefore include the generation and deletion of configurations through recombination.