Congenital transmission (CT) has acquired relevance in Chagas disease (CHD). A cohort of pregnant CHD women (4,355) and their babies were studied in the period 1994–2004. Children were excluded when they had received blood transfusions, or were born or had been in endemic areas; CT rate was 6.1%. Babies were diagnosed between months 1 and 5 in 68.9% of the cases and between months 6 and 12 in 31.1%. In the latter group, parasitemia was detected in 94% and serology in 74.7%. Between months 6 and 9, parasitemia diagnosed 36.2% (P = 0.000) more cases than serology. If serology had been the diagnosis method, those children would have been considered CT free. Taking the overall outcomes, 38.1% of babies were CT free, and 55.8% did not complete the follow-up. Establishing CT as a public health priority and improving first-line health service, congenital CHD coverage could be more efficient in endemic countries.