Formalin-fixed paraffin-embedded (FFPE) tissue blocks are routinely used for histopathological examination and are also useful for specific pathogen detection by polymerase chain reaction (PCR). FFPE tissue is stable at ambient temperature for an extended period of time and relatively easy to transport compared to fresh tissue, which has to be processed or frozen immediately. In addition, archival material is an invaluable source for retrospective molecular and clinical investigation. This chapter describes detailed procedures for nucleic acid extraction and PCR detection of Treponema pallidum using FFPE tissue.