The objective of this work was to test the hypothesis that endurance training may be protective against in vivo doxorubicin (DOX)-induced cardiomyopathy through mitochondria-mediated mechanisms. Forty adult (6-8 weeks) Wistar male rats were randomly divided into the following four groups (n=10/group): not-trained, not-trained DOX (20mg.kg^-1), trained (14-wk endurance treadmill running, 60-90min/day) and trained DOX. Mitochondrial respiration, calcium tolerance, oxidative damage, heat shock proteins (HSP), the activity of antioxidant enzymes, and apoptosis markers were evaluated. DOX induces mitochondrial respiratory dysfunction, oxidative damage, histopathological lesions and trigger apoptosis (p<0.05, n=10). However, training limited the decrease in state 3, respiratory control ratio (RCR), uncoupled respiration, aconitase activity and protein SH content caused by DOX treatment as well as prevented the increased sensitivity to calcium observed in not-trained DOX-treated rats (p<0.05, n=10). Moreover, training inhibited the increase in mitochondrial protein carbonyl groups, malondialdehyde, Bax, Bax/Bcl2 ratio and tissue caspase 3 activity induced by DOX (p<0.05, n=10). Training per se also increased by approximately 2x fold the expression of mitochondrial HSP60 and tissue HSP70 (p<0.05, n=10) and by approximately 1.5x fold the activity of mitochondrial and cytosolic forms of superoxide dismutase (p<0.05, n=10). We conclude that endurance training protects heart mitochondrial respiratory function from the toxic effects of DOX, probably by the improvement of mitochondria and cell defense systems and by a reduction in cell oxidative stress. In addition, endurance training limited the triggering of apoptosis induced by DOX treatment.