Polycystic ovary syndrome (PCOS) is a common endocrine disorder with heterogenous clinical manifestations. The evidence indicates that PCOS is associated with long-term health risks including type 2 diabetes, metabolic syndrome, obstructive sleep apnea, endometrial cancer, and mood disorders. Although cardiometabolic risk factors are more common among women with PCOS, currently there is no strong evidence for increased cardiovascular morbidity and mortality in these patients. The effect of menopausal transition on the long-term health consequences of PCOS is mostly uncertain. The PCOS phenotype improves with aging in affected women. Accordingly, the differences in the cardiometabolic risk profiles of PCOS patients and of the general population seem to disappear after menopause. However, it is not clear whether this phenotype amelioration is associated with changes in other long-term health risks after the menopause. There are also gaps in our knowledge about the impact of long-term use of oral contraceptives on the prevalence of PCOS-related comorbidities. This review summarizes the current knowledge regarding the long-term health consequences of PCOS and their clinical implications in peri- and postmenopause, and highlights areas for future research.