Abstract The U.S. faces a relentlessly growing syphilis epidemic that is concentrated among men who have sex with men (MSM) and transgender (TG) persons. We confront that epidemic with diagnostic tools that have barely changed in over half a century as we continue to rely on serological tests that have a window period from infection to test positivity of 3-5 weeks. This application proposes studies that will use a new, industry- developed experimental transcription mediated amplification (TMA) assay for Treponema pallidum (Tp) both to improve our understanding of the natural history of syphilis, and to assess whether adding TMA testing to serological screening can identify seronegative persons with syphilis in the earliest stage of infection, before serological tests become positive. Our preliminary data suggest that 10% of MSM with syphilis are seronegative, but TMA positive in pharyngeal or rectal specimens. This application builds on that finding. We will initially define the optimal specimen types for TMA testing among persons with active syphilis by comparing TMA positivity in pharyngeal vs. oropharyngeal specimens, and in whole blood vs. serum (Aim 1). Throughout the project, we will test remnant serum, rectal and pharyngeal specimens collected from STD clinic patients diagnosed with syphilis to define how often Tp RNA is present at different anatomic sites in persons with different stages of infection (Aim 2). Finally, we will enroll 3350 MSM and TG STD clinic patients in a prospective study to determine whether adding Tp TMA testing of blood, pharyngeal and rectal specimens leads to earlier identification of syphilis in persons with negative serological tests (Aim 3). For this aim, we will enroll seronegative patients without clinical evidence of syphilis. Participants will receive standard clinical evaluation and treatment at enrollment and will provide the study with serum, rectal and pharyngeal specimens, which the research team will freeze. Twelve weeks after enrollment, we will test these specimens using the TMA, and will contact persons with positive TMA results for interview and repeat serological and TMA testing in order to determine if study subjects developed syphilis or seroconverted since enrollment. Findings from these studies will define how often persons with different stages of syphilis are likely transmissible, and will determine whether screening that integrates serology with TMA testing is superior to standard serological testing alone.