Small duplications (miniduplications) of the D-loop of human mitochondrial DNA (mtDNA) have been described in patients with mtDNA deletions, mtDNA point mutations and in normal aged tissues. The origin of these miniduplications is still unknown but it is hypothesized that they could be formed after oxidative damage. The respiratory chain (RC) is the main source of free radicals in mitochondria and it is believed that a defect in RC increases free radical generation. If miniduplications are originated by oxidative damage, it is expected that they are more abundant in patients with a defect in the RC. We studied the frequency of miniduplications of D-loop in patients with a RC defect due to mtDNA deletions and in controls. We show that four types of miniduplications could be detected with a higher prevalence than in previous studies and that patients with mtDNA deletions did not have higher proportions or increased number of miniduplications, which is against the hypothesis that miniduplications are generated more abundantly in patients with RC defects. We also clearly demonstrate the age-related nature of these miniduplications by a carefully controlled study regarding the age of subjects, which was not considered in other studies on patients with a mitochondrial disease.