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Mitochondrial DNA (mtDNA) plays a key role in the development of a competent oocyte. Mutations of the mitochondrial genome lead to an altered energetic metabolism with negative effects on oocyte developmental competence. In this study, mtDNA heteroplasmy at an intra-oocyte level and between the different analyzed human oocytes (n = 12) was identified by a next-generation sequencing (NGS) protocol previously developed by this research group and submitted to GenBank. This method highlighted, in particular, variants in the genes involved in the respiratory chain providing a direct indication of the cell-specific damage within the mitochondrial genome as predictor of the oocyte quality.