Biogenesis of the oxidative phosphorylation system (OXPHOS) requires the coordinated expression of the nuclear and the mitochondrial genomes. Thyroid hormones play an important role in cell growth and differentiation and are one of the main effectors in mitochondrial biogenesis. To determine how mtDNA expression is regulated, we have investigated the response of two different tissues, the heart and liver, to the thyroid hormone status in vivo and in vitro. We show here that mtDNA expression is a tightly regulated process and that several levels of control can take place simultaneously. In addition, we show that the mechanisms operating in the control of mtDNA expression and their relevance differ between the two tissues, being gene dosage important only in heart while transcription rate and translation efficiency have more weight in liver cells. Another interesting difference is the lack of a direct effect of thyroid hormones on heart mitochondrial transcription.