Background: Syphilis in its different phases may be a difficult diagnosis in clinical and histopathological grounds. Objectives: The present study objectives were to evaluate the detection and tissue distribution of Treponema pallidum in skin lesions of syphilis. Methods: A blinded diagnostic accuracy study was performed with immunohistochemistry and Warthin-Starry silver staining in skin samples from patients with syphilis and other diseases. Patients attended two tertiary hospitals between 2000 and 2019. Prevalence ratios (PR) and 95% confidence intervals (95% CI) were calculated for the association between immunohistochemistry positivity and clinical-histopathological variables. Results: Thirty-eight patients with syphilis and their 40 biopsy specimens were included in the study. Thirty-six skin samples were used as non-syphilis controls. The Warthin-Starry technique was unable to accurately demonstrate bacteria in all samples. Immunohistochemistry showed spirochetes only in skin samples from patients with syphilis (24/40) with 60% sensitivity (95% CI 44.8‒75.2). Specificity was 100% and accuracy, 78.9% (95% CI 69.8‒88.1). Most cases had spirochetes in both dermis and epidermis and there was a high bacterial load. Study limitations: Correlation between immunohistochemistry and clinical or histopathological characteristics was observed but was limited statistically due to the small sample size. Conclusions: Spirochetes were promptly seen in an immunohistochemistry protocol, which can contribute to the diagnosis of syphilis in skin biopsy samples. On the other hand, the Warthin-Starry technique showed to be of no practical value.