IgM immunoblotting and polymerase chain reaction (PCR) were evaluated for use in diagnosing congenital syphilis, and the prevalence of central nervous system (CNS) invasion by Treponema pallidum during congenital infection was examined. The results of rabbit infectivity testing (RIT) on serum and cerebrospinal fluid (CSF) of 19 infants born to mothers with untreated early syphilis were compared with results of PCR and IgM immunoblotting. Seven infants had clinical evidence of congenital syphilis supported by positive serum IgM immunoblot (7/7), PCR (6/7), and RIT (3/3). Six symptomatic infants (86%) had T. pallidum isolated from CSF by RIT; 5 of 6 RIT-positive CSF samples were positive by PCR, and 2 also were reactive by IgM immunoblot. In 12 asymptomatic infants, 5 (42%) had a reactive serum IgM immunoblot and in 4 of these IgM reactivity was the only evidence of congenital infection. CNS invasion by T. pallidum was uncommon among asymptomatic infants; only 1 (8%) was positive by CSF RIT. The excellent agreement between RIT and PCR further substantiates the use of PCR as a surrogate for RIT. Our data indicate that the diagnosis of asymptomatically infected neonates will require a comprehensive approach using assays for both specific neonatal IgM and T. pallidum DNA in serum and CSF.