Epidemiological aspects of syphilis in Western countries have undergone a significant change with respect to the number of cases. Detection of Treponema pallidum is difficult, and the correct diagnosis of secondary syphilis can be critical. In this study, biopsy samples from skin lesions of 12 patients with secondary syphilis were used. Diagnosis of syphilis was based on clinical presentation, dark-field microscope analysis, and serological tests. Using a polyclonal antibody directed against T. pallidum, we show the presence of T. pallidum in 90% of the samples studied with the bacteria located in the epidermis and the upper dermis. The T. pallidum 47-kDa surface protein gene could be amplified by PCR in 75% of the skin lesions. When combining both techniques, T. pallidum was detected in 92% of the samples from patients with secondary syphilis but not in the control samples. Our work suggests that both immunohistochemistry and PCR could be useful for the diagnosis of secondary syphilis and may be helpful in some rare cases when serological assays failed to detect T. pallidum antibodies.