Doxorubicin causes a chronic cardiomyopathy. Although the exact pathogenesis is unknown, recent animal data suggest that somatically acquired alterations of mitochondrial DNA (mtDNA) and concomitant mitochondrial dysfunction play an important role in its onset. In this study, skeletal and myocardial muscles were examined from human autopsies. Compared to controls (n = 8), doxorubicin‐exposed hearts (n = 6) showed low absolute enzyme activity of mtDNA‐encoded nicotinamide adenine dinucleotide hydrogen dehydrogenase (NADH DH, 79% residual activity, p = 0.03) and cytochrome c oxidase (COX, 59% residual activity, p < 0.001), but not of succinate dehydrogenase (SDH), which is encoded exclusively by nuclear DNA. NADH DH/SDH and COX/SDH ratios were 37% (p < 0.001) and 27% (p < 0.001) of controls. Expression of the mtDNA‐encoded subunit II of COX was reduced (82%, p = 0.04), compared to its unchanged nucleus‐encoded subunit IV. MtDNA‐content was diminished (56%, p = 0.02), but the ‘common’ mtDNA‐deletion was increased (9.2‐fold, p = 0.004). Doxorubicin‐exposed hearts harboured numerous additional mtDNA rearrangements lacking direct repeats. They contained elevated levels of malondialdehyde (MDA) (p = 0.006, compared to controls), which correlated inversely with the COX/SDH ratio (r = −0.45, p = 0.02) and the mtDNA‐content (r = −0.75, p = 0.002), and correlated positively with the levels of the ‘common’ deletion (r = 0.80, p < 0.001). Doxorubicin‐exposed hearts also contained the highest levels of superoxide (p < 0.001, compared to controls), which correlated negatively with the mtDNA‐encoded respiratory chain activities, such as the COX/SDH ratio (r = −0.57, p = 0.02) and the NADH/SDH ratio (r = −0.52, p = 0.04), as well as with the mtDNA content (r = −0.69, p = 0.003), and correlated positively with the frequency of the ‘common’ deletion (r = 0.76, p < 0.001) and the MDA levels (r = 0.86, p < 0.001). Doxorubicin‐exposed hearts contained electron‐dense deposits within mitochondria. Hearts exposed to other anthracyclines (n = 6) or skeletal muscle (all groups) had no mitochondrial dysfunction. Doxorubicin, unlike other anthracyclines, augments lipid peroxidation, induces mtDNA mutations and decreases mtDNA content in human hearts. These lesions have an impact on mitochondrial function and could be of importance in the pathogenesis of clinical cardiomyopathy. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.