OBJECTIVE To describe the subgingival microbial profiles of the major putative periodontal pathogens and investigate their role as diagnostic markers for destructive periodontal diseases in an untreated and isolated population. METHODS The source population consisted of all subjects aged ≥ 12 years in an isolated Brazilian population. An interview and a full-mouth clinical examination were conducted and subgingival plaque samples were obtained from four sites per subject. PCR analyses were used to identify the following micro-organisms: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythia, Prevotella intermedia and Campylobacter rectus. RESULTS Among the 214 clinically examined subjects (81% response), 170 of the 195 dentate subjects provided plaque samples. Two subgingival microbial profiles were identified: absence of all micro-organisms but Campylobacter rectus or co-occurrence of Tannerella forsythia and Porphyromonas gingivalis. Using a combination of microbiological and interview information, the smallest overall misclassification in the diagnosis of extensive clinical attachment loss ≥ 5 mm was 8.8% (4.7% of non-cases and 22% of cases), but this was not different from the 7.6% (2.3% non-cases and 24.4% cases) obtained using clinical and interview information (p = 0.292). CONCLUSIONS Specific microbial profiles could be identified in this isolated population. They did not result in significant superior diagnostic accuracy when compared to traditional clinical markers.