In this study, polymerase chain reaction (PCR) techniques were used to detect Treponema pallidum DNA in samples from patients with latent syphilis. Sixty-nine patients with latent syphilis and 18 with treated syphilis were included. Whole blood, plasma, sera and ear scrapings, totalling 235 samples from patients with latent syphilis, were obtained. Three PCR assays (47-PCR, polA-PCR and M-PCR assays) were performed. The 47-PCR yielded the highest number of positive samples -92/235 (39.1%), followed by M-PCR -90/235 (38.3%) and polA-PCR -73/235 (31.1%). Ear scrapings presented the highest number of positives (47/84 -56%), followed by plasma samples (36/84 -42.9%), whole blood (32/84 -38.1%) and sera (21/84 -25%). In conclusion, we have confirmed that T. pallidum can be found in blood of patients with latent syphilis. The 47-PCR technique was found to be the most sensitive, whereas ear lobe scrapings seem to be the best specimen for detection of T. pallidum DNA in latent syphilis.