Polycystic ovarian syndrome (PCOS) is the most common reproductive disorder that affects 6-10% of all women in reproductive age. This syndrome is characterized by clinical or biochemical hyperandrogenism, oligo-anovulation, and polycystic ovaries, with concurrent hormonal and metabolic alterations that alter the follicle maturation and reduce oocyte quality. In vitro fertilization (IVF) has been used as an intervention to improve pregnancy rates. IVF pregnancy outcomes after embryo transfer could remain low due to poor oocyte quality. Embryo selection is mainly based on morphological criteria. However, good morphology of the embryo does not necessarily indicate good functional status, some of these embryos might be genetically abnormal. The change in mitochondrial DNA (mtDNA) copy number is related to the occurrence, severity of PCOS, and oocyte maturation. Mature oocytes usually contain at least 100,000 mtDNA copies, which are necessary for normal development. The number of mtDNA remains stable, and the maintenance of mtDNA copy numbers at an appropriate level is crucial for maintaining mitochondrial function and cell growth. This review summarizes the recent findings for mtDNA as a marker for IVF embryo viability and selection for implantation and predicting pregnancy outcomes