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Objectives: To determine the occurrence of Porphyromonas gingivalis and Aggregatibacter actinomycetemcomitans in patients with periodontal disease using polymerase Chain Reaction.Design: A descriptive cross-sectional study.Setting: The University of Nairobi Dental Hospital.Subjects: Patients presenting at the Oral Diagnosis and Periodontology clinics during the period of the study. The patients had periodontal examination done followed by subgingival plaque collection from selected teeth. DNA extraction from the plaque samples was then done followed by PCR based on Taqman probes using commercially available kits.Results: A total of 92 participants were recruited in the study. Aggregatibacter actinomycetemcomitans (A.a) was found in 14 (15.20%) while Porphyromonas gingivalis (P.g) was present in 16 (17.40%) of the study participants. Based on independent sample t-test, statistically significant positive associations were found between detection frequency of Porphyromonas gingivalis and plaque score (t= 2.47, p= 0.015), gingival index (t= 3.24, p= 0.022), but not with clinical attachment loss (t= 1.90, p= 0.061). Chi square test revealed a positive association between detection rate of P.g and periodontal disease severity (X2= 6.34, p= 0.042). Similar association was also found between detection rate of Aggregatibacter actinomycetemcomitans and increasing age (t=2.19, p= 0.031), clinical attachment loss (t= 4.61, p |