Background: Colombia is an endemic country for Chagas disease, however, it does not have a surveillance program in pregnant women and their children. Migration from rural to urban areas, improvement of vector and transfusion control, and recent reports on some congenital cases suggest the relevance of congenital transmission research. Methods: From January 2010 to December 2011, a cross sectional study was conducted in five endemic departments of Colombia. 4,417 pregnant women were enrolled in primary care institutions. They were tested by ELISA and IFA IgG anti-T. cruzi, and answered a validated questionnaire. A monitoring program was developed. It included home visits, clinical evaluation and laboratory tests -serology, PCR and hemoculture- for positive women and their children, from birth to one year of age. The prevalence of infection in pregnant women, the incidence of congenital cases in children and the risk factors were estimated. A performance evaluation of the program was carried out by measuring timely access to health care, health insurance and tracking cases. Results: Chagas disease was found in 119/4417 women, with overall prevalence of 2.70% (95%CI: 2.0-2.9). The prevalence in each department was: Arauca 2.15% (95%CI: 1.19-3.54), Boyacá 3.20% (95%CI: 1.83-5.18), Casanare 3.97% (95%CI: 2.84-5.28), Meta 0.23% (95%CI: 0.03-0.76) and Santander 3.36% (95%CI: 2.53-4.36). Some factors associated with infection in pregnancy were: older age (p = 0.00), housing conditions (p = 0.00), previous vector contact (p = 0.00), level of education (p = 0.00) and history of Chagas in relatives (p = 0.00). Of 47 children who had completed 12 months of age, 34 (82%) have following up. None has been identified positive by hemoculture or serology. 12.8% (5/39) were positive by PCR, without symptoms. Health insurance, distance from house to hospital, cultural and monetary factors were identified as barriers in health care. Conclusion: Chagas disease in pregnancy is important within rural and urban areas in Colombia. Health insurance problems were identified as barriers to diagnose, treat and monitor Chagas disease in women and newborns. National regulations are needed to achieve coverage for mothers, newborns and relatives.