Introduction: Gastroesophageal reflux disease (GERD) is a common condition and among the most common conditions encountered in GI practice with up to 44% of otherwise healthy Americans suffer from heartburn symptoms at least once a month. Oral manifestations of GERD include halitosis, abnormal taste, mouth ulcerations and dental erosions. Periodontitis results from an interaction between periodontal pathogens, oral microbiota and host immune responses. The relationship between GERD, periodontal microbiota and periodontitis has not been previously performed. Accordingly the aims of the present study is to assess the relationship between GERD and periodontal hygiene using gingival indices and clinical attachment loss as outcome variables while controlling for principle confounding variables in patients with GERD compared to a control group without GERD. Methods: This prospective study was IRB-approved and patients being seen for either GERD or non-GERD conditions in the Gastroenterology Clinic were referred to be seen in the periodontal clinic in a blinded fashion. Subjects were recruited into the GERD arm with a diagnosis of GERD and the presence and frequency of typical GERD symptoms (heartburn, regurgitation, chest pain, and dysphagia) and/or atypical GERD symptoms (coughing, wheezing, hoarseness, and asthma). Subjects in either the GERD or Control arm Eligible were referred to the VAGLAHS Periodontal clinic, where a questionnaire was completed and a comprehensive dental examination was conducted by experienced examiners. Results: 56 patients were enrolled (32 with GERD and 24-aged matched controls). No significant difference between the 2 groups in reference to age, gender, race, income, education level, frequency of dental visits, professional fluoride treatments, fluoridated water history, occupational hazards, alcohol intake, smoking, diabetes, and citrus or soda intake. The GERD group had a statistically significant higher mean erosion index of 0.506 compared to 0.120 of the control group (p-value < 0.01). The highest erosion index in both groups was observed in the upper anterior sextant (test = 0.87, control = 0.34). However, the GERD group had a statistically significant lower mean gingival index of 1.076 compared to 1.385 of the control group (p < 0.01). There was a statistically significant negative correlation between lower gingival index and having a diagnosis of GERD. The GERD group had a statistically significant lower mean plaque index of 0.962 compared to 1.263 of the control group (p-value= 0.01). Conclusion: GERD patients demonstrated more erosion than non-GERD patients. However, GERD patients have less periodontal pathology compared to control subjects. These results suggest for the first time that acidic reflux in patients with GERD have a protective effect on the periodontal microbiota. The role of chronic PPI therapy on periodontal hygiene and microbiota has yet to be explored.