Aim A few studies demonstrated an increased risk of periodontal disease in patients with polycystic ovary syndrome (PCOS). The aim of this study was to evaluate the periodontal status in women of reproductive age who were recently diagnosed with different phenotypes of PCOS. Methods This prospectively designed cross-sectional case-control study included 116 consecutive subjects with PCOS and 90 healthy volunteers, aged between 18 and 24, who were admitted to the gynecology polyclinic between April 2018 and December 2018. All subjects of PCOS diagnosed using the Rotterdam criteria were subdivided into four phenotypes based on clinical, biochemical and ultrasonographic parameters according to the guidelines of the National Institutes of Health. The same dentist investigated periodontal parameters including plaque index, gingival index, bleeding on probing (%), probing depth, clinical attachment loss and the decayed, missing, filled teeth index. Results Probing depth, a periodontal parameter, was higher in all sub-phenotypes of the PCOS group compared to the control group. There was no difference in other periodontal parameters. Conclusion Periodontal probing depth, which is an important parameter in the diagnosis of periodontal diseases, was higher in all phenotypic subgroups of PCOS in early reproductive age.