ABSTRACT Early diagnosis of syphilis plays an important clinical and epidemiological role, since it enables timely treatment and prevents further spread of the infectious agent. Objective — the study was aimed at evaluating the inclusion of biomolecular analysis of material from syphilides of various localizations in the algorithm of clinical and laboratory examination, taking into account the characteristics of sexual contacts. Material and methods. A polymerase chain reaction (PCR) and amplification of ribosomal RNA molecules (NASBA) were used as direct diagnostic methods to detect DNA and rRNA of Treponema pallidum in the samples of biological material from the surface of penile erosion in male patient D. and tonsils, vaginal discharge, and rectum in female patient A. Serological blood tests for the presence of antibodies using non-treponemal (anticardiolipin test/precipitation microreaction [RPR]) and treponemal (enzyme immunoassay [ELISA], passive hemagglutination test [PHA]) tests were used as indirect diagnostic methods. Results. Routine blood test of patient D. detected antibodies to T. pallidum (IgM+G) using ELISA and PHA (titer 1:320), RPR was negative. DNA of T. pallidum (3.27·10³ GE/ml) and rRNA of T. pallidum were detected in the erosive discharge. The results of ELISA test of patient A. for the presence of antibodies to T. pallidum was positive; (PHA) 1:10 240; (RPR) 1:64. The presence of T. pallidum DNA in the samples from tonsillar (4.41·105 GE/ml), vaginal (5.58·102 GE/ml), and rectal mucosa (2.15·104 GE/ml) was detected by PCR. The presence of rRNA of T. pallidum in the material from tonsillar and vaginal mucosa was detected by NASBA. Conclusion. Given the complexity of the diagnosis due to atypical symptoms and extragenital localization of lesions, the use of modern direct highly sensitive methods of laboratory diagnosis of syphilis (PCR and NASBA) along with serological blood tests is a reliable verification of the presence of viable T. pallidum in the studied biological material.