The metabolic and functional diversity of animal mitochondria caused by different mitochondrial compositions due to tissue-specific mitochondrial pathways and tissue-specific differences in expression of isoforms of subunits of enzymes participating in oxidative phosphorylation will be reviewed here. Applying the concept of metabolic control analysis, the relevance of this diversity for the explanation of tissue-specific effects observed in mitochondrial diseases with homoplasmic mitochondrial DNA mutations and nuclear-encoded respiratory chain defects is discussed. Experimental Physiology (2003) 88.1, 149-154.