Congenital toxoplasmosis is an obstetric problem in Mexico, but its actual frequency is unknown. Using a network for screening of non-infectious disorders, we performed a pilot study to determine the frequency of IgM antibodies to Toxoplasma gondii in 1,003 infants (53.1% male, mean +/- SD age = 18.3 +/- 13.0 days, birth weight = 3.116 +/- 0.453 kg) in Mexico City from March to April 2003. Blood samples embedded in filter paper were assayed for IgM antibodies using a capture enzyme-linked immunosorbent assay and results were confirmed by Western blot. Two asymptomatic newborns, one of them premature, had IgM and IgG antibodies in a serum sample taken from both the infant and the mother and were clinically followed. Our data suggest a frequency of approximately two cases of congenital T. gondii infection per 1,000 newborns in Mexico City.