ObjectiveTo investigate Treponema pallidum detection using immunohistochemistry (IHC) and reverse transcription‐polymerase chain reaction (RT‐PCR) assays in acquired oral syphilis (AOS).Materials and MethodsThirty‐seven paraffin‐embedded tissue specimens of AOS (32 secondary and five primary) were analyzed, integrating double‐positive serological results with clinicodemographic and histopathological data. T. pallidum presence was semiquantitatively assessed by IHC, while RT‐PCR targeted T. pallidum DNA. Sensitivity, specificity, and the area under the curve (AUC) were calculated with 95% confidence intervals (CI).ResultsThe study included mostly females (62.2%) with a mean age of 27.1 years. T. pallidum was detected in all samples by IHC, predominantly in the epithelium across all layers (43.2%). RT‐PCR identified T. pallidum DNA in 32 cases, with negative results observed in cases of secondary AOS. The AUC for IHC versus disease stage was 62.5% (95% CI: 45.1–77.8), and for RT‐PCR, it was 57.8% (95% CI: 40.5–73.8). The AUC comparing IHC to RT‐PCR was 83.8% (95% CI: 67.9–93.8).ConclusionThis study represents the first attempt to evaluate the proposed direct detection algorithm for AOS. IHC and RT‐PCR serve as ancillary tools for detecting T. pallidum in both primary and secondary stages of AOS.