Polycystic ovary syndrome (PCOS) is an endocrine disorder that affects up to 10% of the reproductive-aged women worldwide. The etiology is still unknown and treatment therefore remains symptomatic. Studies indicate a possible role of the gut microbiome in the pathology of PCOS. PCOS women have a disturbed gut microbiome, with certain species associated with the PCOS characteristics:hyperandrogenism, ovarian dysfunction, obesity, glucose intolerance and insulin resistance. Although differences have been found in gut microbiome composition between PCOS and healthy women, the literature is inconclusive regarding the difference in gut microbiome biodiversity. Studies examining the vaginal microbiome in PCOS women show consistent results with specific species in the vaginal microbiome. However, there are only few studies on the vaginal microbiome in PCOS women and no studies have yet investigated the correlation between sex-specific hormones and PCOS characteristics. More research is needed to understand the function of the microbiome in the pathophysiology of PCOS, so that this can offer perspectives in future therapies.