Toxoplasma gondii is a parasitic infection that can be transmitted in utero, resulting in fetal chorioretinitis and other long-term neurological outcomes. If diagnosed early, pregnancy-safe chemotherapeutics can prevent vertical transmission. Unfortunately, diagnosis of acute, primary infection among pregnant women remains neglected, particularly in low-and-middle-income countries. Clinically actionable diagnosis is complex due to the commonality of infection during childhood and early adulthood which spawn long-last antibody titers and historically unreliable direct molecular diagnostics. The current study employed a cross-sectional T. gondii perinatal surveillance study using digital PCR, a next generation molecular diagnostic platform, and a maternal-fetal outcomes survey to ascertain the risk of vertical toxoplasmosis transmission in the Western Region of El Salvador. Of 198 enrolled mothers at the time of childbirth, 6.6% had evidence of recent T. gondii infection—85% of these cases were identified using digital PCR. Neonates born to these acutely infected mothers were significantly more likely to meconium aspiration syndrome and mothers were more likely to experience labor and delivery complications. Multivariable logistic regression found higher maternal T. gondii infection odds were associated with the presence of pet cats, the definitive T. gondii host. In closing, this study provides evidence of maternal T. gondii infection, vertical transmission and deleterious fetal outcomes in a vulnerable population near the El Salvador-Guatemala border. Further, this is the first published study to show clinical utility potential of digital PCR for accurate diagnosis of congenital toxoplasmosis cases. Author summary: Toxoplasmosis infection is globally prevalent but can cause severe negative neonatal health outcomes when acquired congenitally. Transmission from mother to neonate depends upon a mother's first-time infection and the stage of pregnancy when mother is infected. The causative agent of toxoplasmosis is a protozoan parasite that contributes to the common difficulties in identifying a mother's primary acute infection. Commonly, serologic testing is administered to identify antibodies to the infection, along with avidity testing that helps to determine current versus past infection. Digital PCR is a next-generation molecular tool that can identify very small quantities of pathogens. This tool was utilized in addition to typical serology plus avidity testing to identify suspected primary T. gondii infections in banked blood and serum samples from Salvadoran women at the time of labor and delivery. Health outcomes surveys were also utilized from the original study to determine associations between recent T. gondii infections during pregnancy and maternal-neonatal pregnancy and birth outcomes. We identified 13 women with evidence of recent T. gondii infection during pregnancy, 11 of which were identified through dPCR. Maternal infection was associated with negative maternal outcomes including pregnancy complications, and associations were found between infection and neonatal meconium aspiration syndrome. Maternal infection was also associated with owning pet cats. This study utilized a new molecular tool to aid in identification of T. gondii primary infection, a neglected disease that is historically difficult to identify through traditional methods. Digital PCR could be useful for toxoplasmosis testing in future studies and clinical settings. [ABSTRACT FROM AUTHOR]