Primary ovarian insufficiency (POI) is a frequently occurring pathology, leading to infertility. Genetic anomalies have been described in POI and mutations in numerous genes have been definitively related to the pathogenesis of the disease. Some studies based on next generation sequencing (NGS) have been successfully undertaken as they have led to identify new mutations associated with POI aetiology. The purpose of this review is to present the most relevant molecules involved in diverse complex pathways, which may contribute towards POI. The main genes participating in bipotential gonad formation, sex determination, meiosis, folliculogenesis and ovulation are described to enable understanding how they may be considered putative candidates involved in POI. Considerations regarding NGS technical aspects such as design and data interpretation are mentioned. Successful NGS initiatives used for POI studying and future challenges are also discussed.