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Objectives: This prospective study focused on the evaluation of anti-parasitic therapy in congenital Chagas' disease, diagnosed and monitored by PCR and conventional diagnosis., Materials and Methods: We studied 152 children born to seroreactive mothers, living in a non-endemic area. Fifty infants aged 0-6 months (GA) were diagnosed by microhaematocrit and PCR and 102 children aged 7 months to 17 years (GB) were diagnosed by serology and PCR. Forty treated patients were monitored for 2 or 3 years by PCR and conventional methods. A competitive-quantitative PCR was used to determine pre-therapy parasitic loads and follow their post-treatment evolution., Results: In GA, the sensitivities of the PCR and microhaematocrit were 100% and 82.4% and their specificities 97% and 100%, respectively. In GB, the sensitivity of the PCR was 73.8% with a specificity of 100%. Pre-therapy parasitic loads ranged from 12.5 to 125,000 and 12.5 to 125 parasite genomic equivalents/mL of blood in GA and GB, respectively. PCR turned negative in all treated pre-therapy PCR positive patients before or at the end of treatment, which was followed by their seronegativation in 10/10 GA, in 3/5 children initiating therapy at 7 months to 2 years of age but in 0/16 initiating therapy at an older age. Two out of the latter patients were occasionally PCR positive during post-treatment, suggesting no parasitological response. Out of nine pre-therapy PCR negative patients, four turned seronegative after treatment, suggesting that in undetermined patients, undetectable parasitic burdens may lead to better post-treatment prognosis., Conclusions: PCR was useful for sensitive diagnosis and therapy monitoring, allowing early detection of refractory cases.