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Background: There is emerging evidence to support the link between polycystic ovarian syndrome (PCOS) and periodontal disease, but the mechanisms associated with these two diseases have not been clearly elucidated but relate to different aspects of inflammation. This study aimed to determine the gingival inflammation indexes and matrix metalloproteinase-9 (MMP-9) in patients with polycystic ovarian syndrome compared to control group.Methods: This is a case-control study in which 87 women referred to the Babol Clinic Private Hospital were divided into three groups: 26 women with PCOS diagnosed on the basis of Rotterdam criteria with gingivitis, 26 women with PCOS without gingivitis and 26 healthy women who were matched for age and body mass index. After recording the underlying variables, fasting saliva samples were taken from all participants in the morning before any periodontal intervention. The samples, which were transferred to Babol Molecular Cell Research Center under cold-chain conditions to measure the serum levels of MMP-9 using ELISA kits. Periodontal status was evaluated for Gingival index (GI), bleeding on probing (BOP), plaque index (PI). Analysis of variance was used to compare the results for the normal quantitative variables and Chi-square test was used to compare the qualitative variables. Significance level was considered less than 0.05.Results: The highest mean periodontal disease indexes (GI, BOP, PI) were observed in women with PCOS with gingivitis and then in women with PCOS without gingivitis and then in healthy women in control group (p <0.05). The mean salivary MMP-9 levels were significantly higher in PCOS women (388/37 ± 75.05) compared to the control group (166/25 ± 35/43). Even in PCOS patients with healthy gingiva (233.00± 47.76) had higher levels of salivary MMP-9 than the control group and this difference was significant (p <0.05)Conclusions: There is a positive association between periodontal disease and PCOS and that salivary MMP-9 levels are higher in PCOS women with and without gingivitis than healthy women. However, it is recommended that multicenter study with larger sample sizes are to be conducted to establish a clearer association.