Early diagnosis of Treponema pallidum infection is helpful for disease management, and conventional PCR is suitable for lesion swabs of patients with probable early syphilis. We thus tested nested and real-time PCR (NR-PCR) in various biosamples from syphilitic patients. Samples were collected from syphilis patients before treatment. Specific primer sequences targeting the T. pallidum gene polA were designed for NR-PCR. Across syphilis types, most samples assayed with NR-PCR returned a positive result, including earlobe blood (92.0%), cerebrospinal fluid (CSF) (90.2%), lesion swabs (74.3%), serum (66.9%), and whole blood (64.2%). No significant differences were observed in positive samples for whole blood, serum, and lesion swabs between primary and secondary syphilis (P > 0.05 for all comparisons). However, more whole-blood samples from patients with secondary syphilis were positive for NR-PCR than whole blood samples from patients with tertiary and latent syphilis (P < 0.05 for all comparisons). For neurosyphilis patients, significantly more earlobe blood samples tested positive than did whole-blood samples (P < 0.05), but there was no difference in positive results for earlobe blood and whole blood in latent syphilis. Significantly more serum samples tested positive in latent syphilis patients with rapid plasma regain (RPR) titers of 1:8 or greater, compared to those with RPR of 1:4 or less. Nested and real-time PCR can be used to identify T. pallidum DNA in biosamples from syphilitic patients, especially earlobe blood.