BACKGROUND: Vertical transmission of Trypanosoma cruzi infection accounts for a growing proportion of new cases of Chagas disease. Better risk stratification is needed to predict which women are more likely to transmit the infection. METHODS: This study enrolled women and their infants at the Percy Boland Women's Hospital in Santa Cruz, Bolivia. Pregnant women were screened for Chagas disease by rapid test and received confirmatory serology. Infants of seropositive mothers underwent diagnostic testing with quantitative polymerase chain reaction (qPCR). RESULTS: Among 5828 enrolled women, 1271 (21.8%) screened positive for Chagas disease. Older maternal age, family history of Chagas disease, home conditions, lower educational level, and history of living in a rural area were significantly associated with higher adjusted odds of maternal infection. Of the 1325 infants of seropositive mothers, 65 infants (4.9%) were diagnosed with congenital Chagas disease. Protective factors against transmission included cesarean delivery (adjusted odds ratio [aOR]: .60; 95% confidence interval [CI]: .36-.99) and family history of Chagas disease (aOR: .58; 95% CI: .34-.99). Twins were significantly more likely to be congenitally infected than singleton births (OR: 3.32; 95% CI: 1.60-6.90). Among congenitally infected infants, 32.3% had low birth weight, and 30.8% required hospitalization after birth. CONCLUSIONS: Although improved access to screening and qPCR increased the number of infants diagnosed with congenital Chagas disease, many infants remain undiagnosed. A better understanding of risk factors and improved access to highly sensitive and specific diagnostic techniques for congenital Chagas disease may help improve regional initiatives to reduce disease burden.