BACKGROUND: Polycystic ovary syndrome (PCOS) is a complex condition with unclear mechanisms, posing a challenge for prevention and treatment of PCOS. The role of the hypothalamus and pituitary gland in regulating female reproduction is critical. Abnormalities in the hypothalamus and pituitary can impair reproductive function. It is important to study hypothalamic and pituitary changes in patients with PCOS. SUMMARY: This article reviews articles on the hypothalamus and PCOS with the goal of summarizing what abnormalities of the hypothalamic-pituitary-ovarian axis are present in patients with PCOS and to clarify the pathogenesis of PCOS. We find that the mechanisms by which the hypothalamus and pituitary regulate reproduction in girls are complex and are associated with altered sex hormone levels, obesity, and insulin resistance. Different animal models of PCOS are characterized by different alterations in the hypothalamus and pituitary and respond differently to different treatments, which correspond to the complex pathogenesis of patients with PCOS. KEY MESSAGES: Arcuate nucleus (ARC) is associated with luteinizing hormone (LH) surges. Suprachiasmatic nucleus, ARC, and RP3V are associated with LH surges. Animal models of PCOS have different characteristics.