Résumé : To better understand the factors involved in maternal-fetal transmission of Trypanosoma cruzi, we compared DNA levels-obtained by use of quantitative real-time PCR and parasitic genotypes determined by PCR amplification followed by hybridization-in Bolivian mothers and their congenitally infected newborns. Mothers and their neonates displayed markedly different parasitic DNA levels, as most maternal estimated parasitemias (> 90%) were < 10 parasites/mL, whereas those of 76% of their newborns were > 1,000 parasites/mL. Comparison of T. cruzi TcII sublineages infecting mothers and newborns showed identity, without evidence of mixed infection in mothers or neonates. Analysis of minor variants of TcIId-genotyped parasites using sequence class probes hybridizing with hypervariable domains of kDNA minicircles showed discrepancies in half of mother/newborn pairs.