Background. Strain typing is a tool for determining the diversity and epidemiology of infections. Methods. Treponema pallidum DNA was isolated from 158 patients with syphilis from the United States, China, Ireland, and Madagascar and from 15 T. pallidum isolates. Six typing targets were assessed: (1) the number of 60-bp repeats in the acidic repeat protein gene, (2) restriction fragment length polymorphism (RFLP) analysis of T. pallidum repeat (tpr) subfamily II genes, (3) RFLP analysis of the tprC gene, (4) determination of tprD allele in the tprD gene locus, (5) the presence of a 51-bp insertion between tp0126 and tp0127, and (6) sequence analysis of an 84-bp region of tp0548. The combination of targets 1 and 2 comprises the Centers for Disease Control and Prevention (CDC) T. pallidum subtyping method. Results. Adding sequence analysis of tp0548 to the CDC method yielded the most discriminating typing system. Twenty-five strain types were identified and designated as "CDC subtype/tp0548 sequence type." Type 14d/f was found in samples from 5 of 6 locations. In Seattle, Washington, strain types changed from 1999 through 2008 (P< .001). Twenty-one (50%) of 42 patients infected with type 14d/f had neurosyphilis compared with 10 (24%) of 41 patients infected with any of the other types combined (P = .02). Conclusion. We describe an enhanced T. pallidum strain typing system that shows biological and clinical relevance. © 2010 by the Infectious Diseases Society of America. All rights reserved.