Using data from the Spanish Collaborative Study of Congenital Malformations (ECEMC), a hospital-based, case-control study and surveillance program, we investigated the potential value of registry systems in the identification of causes of congenital defects when their methodology includes (1) detailed reporting and coding of all anomalies present in each child, whether major or minor, (2) clinical analysis and coding of the global pattern of anomalies present in each infant, and (3) classification of all children studied according to their clinical presentation. These approaches provide great specificity and flexibility in the retrieval and analysis of data. Not only do they permit the study of specific anomalies, but also the analysis of children with MCA patterns, as well as the study of the relationship of specific defects with the rest of the anomalies present in a child. To illustrate this point, we present general data on 15,307 malformed children and more specific information on 153 cases of anal atresia/stenosis identified among the 753,410 live-births surveyed by the ECEMC between April 1976 and September 1989.