Periodontitis is a disease that affects and destroys the tissues that support teeth. Tissues damage results from a prolonged inflammatory response to an ecological shift in the composition of subgingival biofilms. Three bacterial species that constitute the red complex group, Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, are considered the main pathogens involved in periodontitis. In the present study a real-time PCR based assay was designed to detect and quantify red complex species, then used to investigate 146 periodontal pocket samples from 66 periodontitis patients and 80 controls. Results demonstrated a significant higher prevalence of red complex species and increased amount of P. gingivalis and T. denticola in periodontal pocket of periodontitis patients.