Kearns–Sayre syndrome (KSS) is a pleiotropic disorder caused by non-specific spontaneous deletion of a large amount of genetic material from mitochondrial DNA (mtDNA). Aside from patients having mtDNA defects there are also autosomal mutations in nuclear DNA, indicating KSS is not caused by a single gene mutation, but is most likely the result of mutations in genes forming a common biochemical pathway. KSS is characterized by a wide array of symptoms including: ophthalmoplegia, pigmentary retinopathy, ataxia, cardiac conduction defects that later develop into cardiac complications, and brain abnormalities. This review considers the association of deletions in mtDNA with a decrease in mitochondrial function and the pathogenetic role of the dysfunctional mitochondria by analyzing different variants of the mitochondrial genome. Despite there being no curative treatment for these patients, some possible disease modifying therapies have been proposed such as folinic acid supplementation and intravenous arginine therapy.