Objectives: To identify presence of Actinobacillus actinomycetemcomitans (Aa) and Prevotella intermedia (Pi) in subgingival plaque of 3 ethnic groups of selected adult Malaysians with Advanced Chronic Periodontitis using Polymerase chain reaction (PCR) , and to correlate these findings with their clinical periodontal status. Methods: 60 adults, comprising 20 subjects from each ethnic group, participated in this study. In each ethnic group, 10 diseased subjects were age, sex and ethnically matched with 10 healthy individuals. Clinical parameters were assessed for all. Subgingival plaque samples were collected from each subject for identification of Aa and Pi using PCR method. Results: Prevalence for Pi (83.3%) was high and for Aa (6.7%) was low in the total subject population. Pi and Aa were more prevalent in diseased (86.7% and 10% respectively) than in healthy (80% and 3.33% respectively) subjects. Among the different ethnic groups, Aa was detected in 15% of Indian subjects, 5% of Malay subjects but none of the Chinese subjects whereas Pi was detected in 90% of Malay subjects, 85% of Indian subjects and 75% of Chinese subjects. However no significant association between the presence of Aa and Pi with race and disease status was found. Only 5.56% of the infected subjects were colonized by both Aa and Pi. There was no significant association between the presence of Pi and the clinical periodontal parameters. Aa had a moderately significant causal effect on mean CAL (p < 0.05, Observed power = 0.68) when tested by GLM. Conclusion: In this study, detection of Pi was very high but the detection of Aa was low in the diseased as well as healthy subjects. No significant association between the presence of Aa and Pi with ethnicity was detected. Aa had a moderately significant causal effect on CAL. Study supported by Vote F 0130 /2003C, University of Malaya.