A pilot neonatal screening programme revealed a high (approximately 1 per 4800 live births) prevalence of congenital toxoplasmosis (CT) in the State of Rio Grande do Sul, Brazil. The purpose of this paper was to estimate in a larger prospective study the prevalence of CT in the country. At the beginning of the study, an in-house indirect enzyme immunoassay (EIA) was used, to be later replaced with a commercial capture IgM fluorometric enzyme immunoassay (FEIA). Both methods detect specific anti-Toxoplasma gondii IgM-class antibodies eluted from dried blood spots. Of the total of 140,914 samples received from all over the country, 47 cases were identified and confirmed as CT. This finding suggests a prevalence of 1 per 3000 live births. Of the 47 patients, only eight (17%) had clinical manifestations: two had intracranial calcifications, four had retinal scars, one had an intracranial calcification and retinal scars, and one had hepatosplenomegaly with lymphoadenopathy. The testing was paid for by the patients' families who volunteered for the study and gave their informed consent. The 3-year prospective study using sensitive detection methods, reliable confirmation, and feedback from clinicians showed that CT has an extraordinarily high prevalence in Brazil, in fact the highest ever reported in the world. Although the long-term efficacy of treatment of CT has not been well documented, in view of the availability of reliable diagnostics, confirmation and monitoring, functional logistics, and networking for screening, the insidious nature of the sequelae and the very high prevalence of the disease, neonatal screening for CT should be considered an alternative to no screening at all.