Rheumatic diseases and periodontitis are sharing similar pathophysiological features. It is assumed that periodontopathogens could influence the aetiology of rheumatic diseases. However, the underlying pathomechanisms are still unknown. Therefore, we established a specific and sensitive method based on molecular techniques to detect 5 major periodontopathogens, Actinobacillus actinomycetemcomitans (A.a.), Porphyromonas gingivalis (P.g.), Prevotella intermedia, Treponema denticola, Tannerella forsythensis in synovial fluid. Methods: Nine patients suffering from juvenile idiopathic arthritis or rheumatoid arthritis, respectively, were included in this study. DNA from synovial fluid of affected knee joints was isolated by QiaAmp-kit (Qiagen, Hilden, Germany) using an adapted protocol. PCRs specific for the 16S rRNA genes of these bacteria were developed. For positive control of DNA preparation the samples were spiked with E.coli strain XL2B. Subgingival bacterial colonization was analysed using micro-Ident® test (HAIN-Diagnostik, Nehren, Germany). Results: The PCR was optimized in order to detect up to 10 DNA copies of each periodontopathogen. DNA of 2 periodontophatogens, A.a. and P.g., was detected in synovial fluids of two different patients suffering from both juvenile idiopathic arthritis and periodontitis. In the same patients a subgingival infection with P.g. but not A.a. could be detected. Conclusions: For the first time a highly sensitive molecular based detection system was adapted for the identification of periodontopathogens in synovial fluid. The application of this method allows a better understanding of the interaction of periodontitis and rheumatic diseases. The revealed first results indicate that periodontopathogens may play a role in the pathway of rheumatic diseases. Keywords: periodontitis, rheumatic disease, periodontopathic bacteria