The potential co-amplification of actual mtDNA and nucleus-embedded mtDNA sequences was studied for the mtDNA domains encompassing the major disease-causing mtDNA mutations. By using two different cell lines devoid of mtDNA (rho degree cell lines), it is shown that nucleus-embedded mtDNA sequences readily co-amplified with most of the mtDNA domains encompassing disease-causing mtDNA mutations. The selection of mtDNA primers for specificity on rho degree cells constitutes a simple procedure to avoid such co-amplification. It appears mandatory prior to quantify mtDNA mutations, especially when delivering prenatal diagnosis or predictive genetic advise.