Restriction fragment analysis of mitochondrial and chloroplast DNAs from a brown anther and a petaloid cytoplasmic male-sterile (cms) line revealed unique patterns for each cms line distinct from those of normal fertile cytoplasms, but identical restriction fragments for all chloroplast DNAs. The restauration of fertility through the introduction of nuclear restorer genes had no effect on the overall mitochondrial DNA (mtDNA) structure. The genomic environment and transcription patterns of several mitochondrial genes differ between cms and normal cytoplasms, while no difference has so far been detected between cms and the corresponding fertility-restored lines in mitochondrial DNAs and mRNAs. Mitochondrial translation products analysed by in-organello synthesized proteins revealed a number of polypeptides unique to each cytoplasm. Most prominent is a 17-kDa polypeptide that is present in the brown anther cms line but not in fertile mitochondria. Synthesis of this protein was not visibly affected by fertility restauration. The different cms phenotypes in carrot are thus associated with extensive and unique mtDNA rearrangements and distinct alterations in transcription and translation patterns.