Background: Microbiological identification of Aggregatibacter actinomycetemcomitans and other periodontal pathogens may depend on the test protocol, especially if the concentration is near the lower detection threshold. The goal of the current study was to compare the results of the microbiological testing with different test-kits in patients with severe chronic (CP) and aggressive periodontitis (AgP). Methods: 69 Patients were recruited in the Section of Periodontology, University Hospital of Heidelberg. Inclusion criterium to participate in the study were the clinical diagnoses CP or AgP. Pocket probing depths, vertical attachment level, gingival bleeding index, plaque control record and bleeding on probing were assessed by a periodontologist. Microbiological analysis of pooled samples from subgingival plaque was performed with two different gene probe-tests according to the manufacturer's test protocol (IAI PadoTest 4.5®, Institut für Angewandte Immunologie, Zuchwill, Switzerland (PADO), and the Meridol® Periodiagnostics, GABA, Lörrach, Germany (MERI). Results: CP was diagnosed in 49 patients, AgP in 20 patients. The periodontal pathogens Aggregregatibacter actinomycetemcomitans (A.a.), Tannerella forsythia, Porphyromonas gingialis and Treponema denticola) were identified with both PADO and MERI: Fusobacterium nucleatum and Prevotella intermedia were only assessed by MERI. With the loboratory real-time PCR-test A.a. was identified. in series 1 more patients ware tested positive on A.a. with MERI (25%) than with PADO (20.6%). In series 2 the real-time PCR (23.2%) showed a lower prevalence for A.a. than PADO (36.4%). Only 10.3% of the patients in series 1 and 17.2% of the patients in series 2 were tested positive on A.a. with both tests. The used tests showed an agreement of k=0.72 for series 1 and k=0.41 for series 2. The test-differences for the rest bacteria-species were smaller or barely present. Conclusions: The use of a high sensitive microbiological test is important for the choice of an optimal adjunctive antibiotic treatment. In the underlying study both commercial and laboratory microbiological tests showed an incongruence regarding the identification of A.a. Differences between the tests were also proven for the qualitative microbiological detection. Keywords: periodontitis, microbiological testing, periodontal pathogens, aggregatibacter actinomycetemcomitans