AIM: This study sets out (a) to estimate the prevalence of admissions by birth defects, using the official database of hospitals of Ecuador; and (b) to set the basis for a new National Register of Birth Defects in Ecuador that works as a program for the clinical and epidemiological investigation of risk factors in the etiology of congenital anomalies in Ecuadorian hospitals, using a case-control methodological approach. This is the first report in their class. METHODS: The data used in this study are derived from the National Register of Hospital Admission/Discharges of the Instituto Nacional de Estadísticas y Censos; data of the Ministry of Public Health were also used. Ecuador does not have an official Medical Birth Registry or a Congenital Malformations Registry. RESULTS: A total of 51,375 discharges by congenital malformations were registered in a 7-year period. Of these, 16,679 admissions were of children aged less than 1 year of age, with a birth prevalence rate (BPR) of 72.33/10,000 births. 77% of the congenital defects registered comprise the 50 most common birth defects observed in this age group. Cleft lip was the most prevalent birth defect in children less than 1 year of age and the second most common defect in children 1 to 5 years of age. Unilateral cleft lip shows a BPR of 4.57/10,000 births; cardiac birth defects as a group have a BPR of 4.2; hydrocephalus a BPR of 3.77; and Down's syndrome a BPR of 3.70. Undescended testicle was the most prevalent birth defect in children between 1 to 5 years. 9384 children under 1 year of age were male (55.9%) and 7053 were female (42.1%). BPR in males was 40.45 and in females 30.40. CONCLUSION: This report documents the prevalence estimates for birth defects reported in the hospital discharge data. These estimates are important to 1) plan for health-care and education needs of the Ecuadorian population, 2) identify increased occurrences of birth defects in specific geographic regions, 3) serve as a reference point for assessment of provincial surveillance systems, 4) evaluate national public health interventions, 5) compare Ecuador prevalence estimates with those of other countries, and 6) help determine the appropriate allocation of resources for basic and public health research. There is an urgent need to establish a National Registry of Birth Defects involving different sources of information such as prenatal medical records, birth records and medical records during the first year of life at an early stage, and surveys on cytogenetic prenatal diagnostic surveys and cytogenetics of therapeutic abortions.