Congenital syphilis (CS) can occur when a mother is inadequately treated or not treated at all for an active Treponema pallidum infection. Symptoms of CS are often subtle and non-specific, and it is estimated that up to 60% of affected infants are asymptomatic at birth, making the diagnosis dependent on laboratory findings. Despite decades of experience with CS, problems still arise in its diagnosis because laboratory test results for children at risk for CS can be inconclusive and no single diagnostic test can be used to diagnose CS. The development of diagnostic tests such as enzyme immunoassays, immunoblotting and polymerase chain reaction (PCR) has increased the sensitivity and specificity of diagnoses, but the detection of specific IgM is currently the most sensitive serological method, and the presence of specific IgM should be considered as evidence of a congenital T. pallidum infection. Suspected cases can also be confirmed or excluded by serial post-partum tests of antibody kinetics. The authors note strongly that it is considered unethical not to treat a baby at risk of contracting CS, even without a definitive diagnosis. In this review, we describe the various microbiological methods-and their shortcomings-used in the laboratory diagnosis of CS.