BACKGROUND: The National Birth Defects Prevention Network collects state-specific birth defects surveillance data for annual publication of prevalence estimates and collaborative research projects. In 2006, data for 21 birth defects from 1999 through 2001 were presented as national birth prevalence estimates. The purpose of this report was to update these estimates using data from 2004 through 2006. METHODS: Population-based data from 11 active case-finding programs, 6 passive case-finding programs with case confirmation, and 7 passive programs without case confirmation were used in this analysis. Pooled birth prevalence estimates for 21 birth defects, stratified by case ascertainment approach, were calculated. National prevalence estimates, adjusted for maternal race/ethnicity and maternal age (trisomy 13, trisomy 18, and Down syndrome only) were determined using data from 14 programs. The impact of pregnancy outcomes on prevalence estimates was also assessed for five specific defects. RESULTS: National birth defects prevalence estimates ranged from 0.72 per 10,000 live births for common truncus to 14.47 per 10,000 live births for Down syndrome. Stratification by type of surveillance system showed that active programs had a higher prevalence of anencephaly, anophthalmia/microphthalmia, cleft lip with or without cleft palate, reduction defect of upper limbs, and trisomy 18. The birth prevalence of anencephaly, trisomy 13, and trisomy 18 also varied substantially with inclusion of elective terminations. CONCLUSION: Accurate and timely national estimates of the prevalence of birth defects are needed for monitoring trends, assessing prevention efforts, determining service planning, and understanding the burden of disease due to birth defects in the United States. Birth Defects Research (Part A), 2010. © 2010 Wiley-Liss, Inc.