BackgroundDespite conflicting results on the use of hormone replacement therapy (HRT) there is no doubt that many women benefit from it. Women using HRT are known to be more health conscious in general with putative positive implications in the mouth. However, we observed recently in our cohort hardly any difference in oral health status between HRT-users and non-users. There are only a few studies about HRT and oral microbiota. We hypothesized that counts of periodontal micro-organisms are lower in health-conscious HRT-users than non-users.MethodsTwo-year open follow-up study was conducted on originally 200 HRT-users and 200 non-users from age cohorts of 50-58 years. After clinical examination pooled subgingival plaque samples were taken for polymerase chain reaction analyses. The results of finally 135 women meeting the inclusion criteria were analyzed with cross-tabulation and chi-square test. Explanatory factors were studied by step-wise logistic regression analysis.ResultsIn HRT group, the numbers of positive samples for Porphyromonas gingivalis (P. gingivalis, p < 0.07), Prevotella intermedia (P. intermedia, p < 0.05)and Tannerella forsythia (T. forsythia, p < 0.01) decreased in women with ≥ 4-mm-deep pockets. Respectively in HRT users with ≥ 6-mm-deep pockets the numbers of positive samples for P. gingivalis (p < 0.05) and T. forsythia (p < 0.01) were decreased. No corresponding differences were observed in the non-HRT group. In logistic regression, the existence of deep periodontal pockets explained the majority of cases harboring specific micro-organisms in both groups.ConclusionAlthough use of HRT did not correlate with periodontal health status, HRT led to decreasing numbers of positive samples of the periodontal pathogens P. gingivalis and T. forsythia. Further studies with longer observation time are needed to observe the clinical relevance of the results.