The nonchromosomal stripe (NCS) mutations of maize are a set of maternally inherited mutations that result in reduced plant growth and lowered reproductive capacity. NCS6 mutants are characterized by stunted growth, yellow stripes on leaves, and sectors of aborted kernels on ears. The heteroplasmic NCS6 striped plants carry both partially deleted and normal versions of the mitochondrial cytochrome oxidase subunit 2 (cox2) gene and have low levels of cox2 transcripts when compared with nonstriped control plants. Other tested mitochondrial genes and their transcripts appear to be unaltered in NCS6 plants. The level of COXII protein is also specifically reduced in the striped plants relative to that of control plants. In the NCS6 mutant mitochondrial genome, a portion of the first exon of the cox2 gene is deleted along with the 5' flanking region. The formation of the defective cox2 gene appears to have involved a recombination event between 31-bp repeats.