Mothers pass T. cruzi on to their children as T. cruzi travels through the placenta, birth canal, and possibly maternal milk. This type of transmission occurs less frequently than other methods. In general, rates of congenital infection are less than 10%, although this rate is much higher in endemic areas like Bolivia. The congenital rate has increased over the years.

Mechanisms of transmission of infection from mother to child are unknown. Possibilites include diffusion of the parasite across the extra-embryonic membranes, or through the maternal blood supply. Serious threats are posed to the fetus by high toxicity levels of nifurtimox and benzidazole, the known medications that fight T. cruzi. Infection is difficult to detect in the unborn.