Our knowledge of mitochondrial biology has advanced significantly in the last 10 years. The effects of mitochondrial dysfunction or cytopathy (MC) on the heart and neuromuscular system are well known, and its involvement in the pathophysiology of several common clinical disorders such as diabetes, hyperlipidaemia and hypertension, is just beginning to emerge; however, its contribution to renal disease has received much less attention, and the available literature raises some interesting questions: Why do children with MC commonly present with a renal phenotype that is often quite different from adults? How does a mutation in mitochondrial DNA (mtDNA) lead to disease at the cellular level, and how can a single mtDNA point mutation result in such a variety of renal- and non-renal phenotypes in isolation or combined? Why are some regions of the nephron seemingly more sensitive to mitochondrial dysfunction and damage by mitochondrial toxins? Perhaps most important of all, what can be done to diagnose and treat MC, now and in the future? In this review we summarize our current understanding of the relationship between mitochondrial biology, renal physiology and clinical nephrology, in an attempt to try to answer some of these questions. Although MC is usually considered a rare defect, it is almost certainly under-diagnosed. A greater awareness and understanding of kidney involvement in MC might lead to new treatment strategies for diseases in which mitochondrial dysfunction is secondary to toxic or ischaemic injury, rather than to an underlying genetic mutation.