The aim of the study was to determine the prevalence of Treponema denticola in saliva of periodontally diseased and healthy patients and its relationship with the periodontal status. A 16S rRNA-based polymerase chain reaction detection method was used to determine the prevalence of T. denticola in whole saliva samples from patients with chronic periodontitis (CP, n = 37), aggressive periodontitis (AgP, n = 24), and healthy subjects (n = 28). The periodontal status of each subject was assessed by criteria based on probing depth, clinical attachment loss, and extent of periodontal breakdown. Risk factors were assessed individually and adjusted for confounding using a binary logistic regression model. The results showed that the prevalence of T. denticola in CP patients was significantly higher than those in healthy and AgP subjects (P < 0.05). Odds ratio analysis revealed a positive association for CP group/T. denticola-positive and smoking/T. denticola-positive subjects. Furthermore, all clinical measurements were significantly greater (P < 0.05) for T. denticola-positive subjects compared to T. denticola-negative subjects. After binary logistic regression analysis, both T. denticola and smoking were independently and strongly associated with development of CP. It was concluded that when used in conjunction with an optimized clinical examination protocol, this assay may offer a rapid, useful, and cost-effective tool for monitoring the presence of T. denticola in noninvasive clinical samples from both healthy and diseased patients and correlating it with the amount and extent of periodontal breakdown.