Polycystic ovary syndrome (PCOS) is a common and complex endocrine disorder. Emerging animal and human data point out to various changes in microbiota that could be linked with the syndrome. However, the effects of therapeutic approaches on gut microbial composition in women with PCOS remain unknown.We aimed to assess whether gut microbial composition is altered in PCOS and to determine potential impact of oral contraceptive (OC) use on gut microbiota.Prospective observational study.Tertiary referral hospital.The study included 17 overweight/obese patients with PCOS and 15 age- and BMI-matched healthy control women.At baseline, clinical, hormonal and metabolic evaluations and gut microbial composition assessment by 16S rRNA gene amplicon sequencing were performed for both groups. All measurements were repeated in patients after receiving an OC along with general lifestyle advice for three months.Alpha and beta diversity did not show a difference between patients with PCOS and healthy controls at baseline and remained unaltered after 3 months of OC use in the PCOS group. Relative abundance of Ruminococcaceae family was higher in PCOS (p=0.006) and did not show a significant change after treatment.Women with PCOS have increased abundance of Ruminococcaceae whereas short-term OC use does not alter compositional features of gut microbiota in the syndrome.