This study compared the validity of birth defect cases reported in the Brazilian Information System on Live Births in 2004 and 2007 in seven municipalities, out of a total of 27,945 live births in 2004 and 25,905 in 2007. The study also describes quality improvement measures in this area. The Latin American Collaborative Study on Congenital Malformations was used as the gold standard for analyzing the validity of birth defect diagnoses. In 2004, at least 40% of birth defects went unreported, and this situation persisted in 2007. Only one hospital showed a significant increase in reporting sensitivity, from 56.9% to 96.8%. Sensitivity decreased significantly in two hospitals (from 62.7% to 41.75% and from 66.5% to 32.2%, respectively). The positive and negative predictive values and specificity remained above 80%. Only two municipal health departments and four hospitals implemented measures to improve reporting of birth defects. The results indicate the need for investments in the quality of birth defect information on birth certificates.