Treponema pallidum subspecies pallidum is the causative agent of syphilis, a sexually transmitted disease that still represents a major world health problem. Serology, the standard laboratory method used for the diagnosis of syphilis, has several limitations that preclude reliable diagnosis of syphilis in some cases. Direct methods of syphilis diagnosis are suboptimal because of low sensitivity and low specificity (microscopy), or because of costly and delayed test results (rabbit infectivity test). Recent status of PCR-based syphilis diagnosis and molecular typing schemes are reviewed. PCR detection of Treponema pallidum in various clinical samples showed high sensitivity, specificity and potential for molecular typing. PCR diagnosis is therefore considered an important auxiliary laboratory test for syphilis. Typing of Treponema pallidum strains isolated from patients will stimulate epidemiological studies of syphilis and will allow discrimination between re-infection and reactivation of infection.