A molecular system was used to subtype Portuguese Treponema pallidum clinical strains isolated from both skin lesions and blood. The study with this system constitutes the first typing study in a European country. Three T. pallidum subtypes were found: subtypes 14a (50%), 14d (45.2%), and 14f (4.8%). Further studies are needed to better characterize the isolates involved in syphilis outbreaks.Syphilis, caused by the spirochete Treponema pallidum subsp. pallidum, is a multistage disease with a wide spectrum of clinical manifestations (8). Of particular relevance to public health is the recognition that syphilis increases the risk of transmission and acquisition of the human immunodeficiency virus (6). Until the end of the 20th century, the in vitro noncultivable condition of T. pallidum, allied with the high GC content of major portions of its genome (5), prevented the success of any strategy for the typing of T. pallidum clinical isolates. In 1998, Pillay et al. (13) made a very important step toward obtaining an understanding of the molecular epidemiology of T. pallidum by developing the only existing method for the genotyping of this pathogen. The method is based on the intrastrain variability of the acidic repeat protein gene (arp) and the Treponema pallidum repeat gene (tpr). To date, the laboriousness and low sensitivity of this procedure have limited its application to only five published studies (11,(13)(14)(15)17), focused mainly in two countries, South Africa and the United States. Consequently, there are only 288 typed T. pallidum strains worldwide (11,(13)(14)(15)17), which is a strikingly small number, considering the predicted syphilis incidence rate (18). In Portugal, early and congenital syphilis require mandatory notification (4); nonetheless, as in the rest of Europe, there is a complete lack of awareness of the diversity of the circulating T. pallidum strains. Here we report the results of a pioneer study in which we used the recent subtyping system developed by Pillay et al. at the Centers for Disease Control and Prevention (13) in order to identify and differentiate Portuguese T. pallidum isolates.Four hundred sixteen individuals (104 women and 312 men) suspected of having early syphilis (on the basis of clinical data and serology), most of whom were attending the major Portuguese sexually transmitted disease clinic (located at the Lapa Health Centre in Lisbon, Portugal), were evaluated for T. pallidum infection between 2004 and 2007. T. pallidum DNA was extracted from skin lesions or blood samples by using a QIAamp DNA mini kit (Qiagen, Valencia, CA), according to the manufacturer's instructions. T. pallidum was detected in 86 specimens (35 primary and 7 secondary lesions and 44 blood samples) by using a commercially available real-time PCR assay (Sacace, Caserta, Italy) that targets the gene coding for a recognized T. pallidum surface antigen, the 39-kDa basic membrane protein (bmp; locus TP1016 relative to the sequence of T. pallidum strain Nichols, GenBank accession number NC_000919 [3,5]...