The human body hosts a large variety of microorganisms in high numbers. Understanding the characteristics of these microorganisms and their interactions with the human body is the topic of the Human Microbiome Project. Following the same goals, this study was conducted to understand the interactions between microorganisms in the human oral cavity and inflammatory processes related to rheumatism. Previous findings suggest a correlation between periodontitis and the occurrence or severity of rheumatoid arthritis. In order to investigate this hypothesis, a suitable detection method for several periodontal pathogens needed to be defined. The microorganisms in question were: Aggregatibacter actinomycetemcomitans, Campylobacter rectus, Eikenella corrodens, Porphyromonas gingivalis, Prevotella denticola, Prevotella nigrescens, Streptococcus mutans, Tannerella forsythia and Treponema denticola. Supragingival plaque samples were analysed by real-time PCR and the obtained results cross-checked by agarose gel electrophoresis. Except for C. rectus and P. nigrescens, all microorganisms were detected with two different primer systems. In almost all cases, the results obtained by real-time PCR were confirmed by the agarose gel electrophoresis. The method is to be modified though, in case quantitative results are desired. For the detection of the microbiome present in the human oral cavity, it is advised to use a method that allows high throughput at low costs.