Background DNA from many pathogens can be detected in saliva. However, the presence and quantity of Treponema pallidum DNA in syphilis patients in saliva is unknown. Methods A total of 234 syphilis patients with different stages and 30 volunteers were enrolled. Paired saliva and plasma samples were collected from all the participants. Consecutive saliva samples from 9 patients were collected every 4 hours following treatment. Treponema pallidum DNA in samples was determined by nested PCR and droplet digital PCR targeting polA and Tpp47. Results Treponema pallidum DNA detection rates in saliva and plasma were 31.0% (9/29) and 51.7% (15/29) in primary syphilis(p=0.11), 87.5% (63/72) and 61.1% (44/72) in secondary syphilis(p<0.001), 25.6%(21/82) and 8.5%(7/82) in latent syphilis (p=0.004), 21.6%(11/51) and 5.9%(3/51) in symptomatic neurosyphilis (p=0.021), respectively. The loads of Tpp47 and polA in saliva were median 627 copies/ml (range, 0-101200 copies/ml) and median 726 copies/ml (range, 0-117260 copies/ml) for syphilis patients, respectively. In plasma, however, the loads of Tpp47 and polA were very low: median 0 copies/ml (range, 0-149.6 copies/ml) and median 0 copies/ml (range, 0-176 copies/ml), respectively. The loads of Treponema pallidum DNA in saliva during treatment were fluctuating downward, and the clearance time was positively correlated with the loads of Treponema pallidum DNA before treatment. Conclusions The collection of saliva is noninvasive and convenient. The high loads of Treponema pallidum DNA in saliva and the reduction after treatment indicated that saliva can be not only a diagnostic fluid for syphilis, but also an indicator of therapeutic effectiveness.

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