A deletion eliminating part of a transcribed region of mitochondrial DNA (mtDNA) has been found in the maize nonchromosomal stripe 3 (NCS3) mutant. This results in the specific loss of a set of three mitochondrial RNAs consisting, in normal plants, of a 4.9 kb transcript, its 1.8 kb intron and the resulting processed mRNA of approximately 2.9 kb. In the NCS3 mitochondrial genome the DNA encoding the putative promoter and 5' end of the affected RNAs is missing. This transcribed region of normal maize mtDNA has been sequenced and the intron splice junction has been determined. The 2.9 kb processed mRNA carries two overlapping open reading frames (ORFs) with predicted amino acid sequences that show similarity to two Escherichia coli ribosomal proteins, S3 (rps3) and L16 (rpl16). The presence of severe stunting and striping in NCS3 plants correlates absolutely with the molecular changes described here. This fact and the impaired ability for mitochondrial protein synthesis by NCS3 plants indicate that one or both of these reading frames are translated to functional ribosomal proteins in normal maize mitochondria.