It is now clear that molecular defects in human mitochondrial DNA play a significant role in human disease. Mitochondrial DNA mutations range from single base changes in the 16.5 kilobase-pair genome up to large deletions and rearrangements. Independently of the actual cause of a given mutation, it is possible to predict at least some of the consequences of changes in mitochondrial DNA sequence. This paper reviews our overall understanding of the mode and mechanism of mitochondrial DNA replication and transcription and how this relates to mitochondrial gene expression. This provides a background to anticipate the nature and extent of mitochondrial DNA sequence changes that might be of physiological consequence.