Objectives This study aimed to obtain nationally representative estimates of HIV and syphilis prevalence and coverage of preventive antenatal services in pregnant women in Ecuador, in order to develop a national strategy for the elimination of mother-to-child transmission of HIV and syphilis.

Methods A national probability sample of 5988 women presenting for delivery or miscarriage services was selected from 15 healthcare facilities during 2011–2012, using a two-stage cluster sample technique. Biological specimens were collected and an interview and review of medical records were performed. Agreement between these last two sources was measured. Estimates were adjusted for the sampling design.

Results Estimated national HIV prevalence (0.60%) was higher than confirmed syphilis infection prevalence (0.25%). In the coastal region, HIV prevalence (1.13%) exceeded the threshold that defines a generalised epidemic and syphilis prevalence reached 0.37%. An estimated 5.9% of women did not use antenatal care services while 73.0% completed at least four consultations. HIV testing coverage (89.9%) was higher than for syphilis (71.6%). Agreement between medical records and interviews was mostly moderate (0.40–0.75). Important variables were frequently not recorded, such as timing of syphilis testing, which was not recorded in 49.6%.

Conclusions The concentration of HIV and syphilis infections in the coastal region of Ecuador highlights the need for intensified prevention and a response tailored to local epidemic conditions. Major challenges for the elimination initiative include achieving universal, early access to antenatal care, improving coverage of HIV and syphilis testing, and improving the quality of medical records to support progress monitoring.