The human oral flora consists of a highly diverse, interactive community. The resident microflora live in harmony with its host but changes such as poor oral hygiene, diet and stress perturb microbial balance found in health and promote the growth of organisms associated with plaque-mediated diseases. Detection of bacterial rRNA genes for the presence of bacteria is a well-established technique. PCR amplification of rRNA genes has been used successfully to detect and identify bacteria that cause a variety of infections. Objective: To correlate bacterial type and number with dental pathology, we have developed species-specific 16S rDNA-directed real-time PCR assays for the quantitative identification of oral bacteria. Methods: Fifteen sets of oligonucleotide primers and probes were designed from nucleotide sequence information available from GenBank. Amplification and detection were performed with the ABI PRISM 7700 sequence detection system. A standard curve was plotted for each primer-probe set by using Ct values obtained from amplification of known quantities of DNA. Linearity of the detection system was determined by amplification of successive 10-fold DNA dilutions in a series of real-time PCRs. PCR assay specificities were tested against reference oral strains. Results: All 15 organisms tested which included Actinomyces naeslundii, Eikenella corrodens, Fusobacterium nucleatum, Haemophilus actinomycetemcomitans, Lactobacillus acidophilus, Micromonas micros, Porphyromonas gingivalis, Prevotella intermedia and Streptococcus mutans were correctly identified when compared with the reference oral strains used. Bacterial detection was linear over a large range of DNA concentrations (correlation coefficient = 0.96). The lower limits of detection were 10-100 CFU or 10 fg depending on the species. There were no cross-reactivities with heterologous DNA of bacterial strains tested. Conclusion: These results indicate the PCR assays developed are useful for rapid, species-specific, quantitative identification of oral bacteria.