Early diagnosis of congenital Trypanosomacruzi transmission in newborns is essential because babies show high indices of cure. Conventional diagnosis is based on microscopic examination and serology. Molecular diagnosis is a promising alternative to replace conventional diagnosis, although it is not well suited for adoption in laboratories with limited resources. Isothermal DNA amplification methods have the advantage of not requiring expensive equipment. The aim of this work was to apply loop-mediated isothermal amplification (LAMP) to detect congenital infection in babies colorimetrically. This assay was able to detect all T. cruzi discrete typing units and Leishmania braziliensis, but not other pathogens. The assay showed a limit of detection of 50 parasites/mL in spiked artificial samples. This assay was tested in 27 blood samples of babies born to T. cruzi-infected mothers and showed 100% of concordance with conventional diagnosis. This is the first study to detect T. cruzi in clinical samples by LAMP, showing that this assay would be useful in the detection of congenital T. cruzi infection. The advantages of this novel tool include the speed with which the assays can be completed, the no-need of trained personnel, and the fact that it can be performed without complex and expensive laboratory equipment.