The authors hypothesized that changes in prenatal factors such as termination of pregnancy for fetal anomalies and prenatal vitamin supplementation have altered the epidemiology of patients with multiple congenital anomalies and may have had an impact on their prevalence in the current era. This study reviewed the Nationwide Inpatient Sample database from 1998 to 2008 and compared the prevalence of ECM among live births with a CHD diagnosis (case) and that among live births without a CHD diagnosis (control). For this study, 42 ECM and 10 CHD diagnoses were selected for subanalysis. Longitudinal analysis also was performed to determine temporal variation of ECM prevalence in the CHD population during the 11-year study period. The cohort in this study consisted of 97,154 patients in the case group and 12,078,482 subjects in the control group. The prevalences in the CHD population were 11.4 % for nonsyndromic congenital malformation (NSCM), 2.2 % for genetic syndrome (GS), and 13.6 % for overall extracardiac congenital malformation (ECM). The prevalences in the control group were 6.7 % for NSCM, 0.3 % for GS, and 7.0 % for ECM. The findings showed a strong association of NSCM [odds ratio (OR) 1.88; 95 % confidence interval (CI) 1.73–1.94], GS (OR 2.52; 95 % CI 2.44–2.61), and overall ECM (OR 2.01; 95 % CI 1.97–2.14) with CHD. The prevalences of GS and multiple organ system CM decreased significantly during the study period. This study was the largest and most comprehensive population-based study to evaluate the association between CHD and ECM in newborns.