Polycystic ovary syndrome (PCOS) is an endocrine disorder that affects woman’s ovaries and reproductive system. PCOS is considered a challenging disorder for the physicians due to the continuous need for treatment modifications based on the patient’s needs and preferences throughout her lifetime. The main cause of PCOS is unknown but a combination of several parameters including genetic and/or epigenetic factors, environmental factors, exposure to high levels of androgen prenatally and the hypothalamic pituitary-ovarian axis and adrenal dysfunction may play a role in the onset of the syndrome. PCOS is characterized by many metabolic, reproductive and hormonal disorders. Also, early diagnosis and treatment have a great importance to prevent many complications such as insulin resistance (IR), obesity, diabetes mellitus (DM), infertility, cardiovascular disease and even endometrial cancer. In the ovary, vitamin D was found to stimulate the production of progesterone and estradiol. Also, the presence of vitamin D3 in the follicular fluid and the expression of VDR in granular cells were confirmed. This fact suggests that vitamin D3 may be important in folliculogenesis, but it has not yet been clearly confirmed. Scientists claimed that, similarly to skin cells, in granular cells, vitamin D3 can stimulate the activity of aromatase, responsible for the conversion of androgens to estrogens, which would prove the role of vitamin D3 in folliculogenesis and ovulation. Moreover, vitamin D deficiency was reported to be common in women with PCOS. So, it was suggested that the metabolic changes in PCOS are related to dysfunction of vitamin D and calcium metabolism, which is important in follicular development and normal glucose metabolism. The relationship between PCOS and the gut microbiomes has emerged recently, and they were thought to play a role in the development of the syndrome. Environmental factors that drive the gut microbial community to become dysbiotic were supposed to make them playing a pathogenic role in the onset and progression of PCOS. Distinct microbiota were responsible for distinct pathogenic elements of PCOS. Women with PCOS were reported to have altered intestinal flora compared to healthy controls. This alteration was related to a decrease in α diversity and changes in β diversity. It has been found that there is a link between lower alpha diversity of gut microbiota and obesity, which is one of the most important comorbidities of PCOS in women