BACKGROUND There is a known association between congenital heart disease (CHD) and other congenital anomalies (CA). These associations have been altered by changes in prenatal factors in recent time. We reviewed the largest database of inpatient hospitalization information and analyzed the current association between common CHD diagnoses and other congenital anomalies. METHODS Case-control study design. We reviewed the Nationwide Inpatient Sample (NIS) database from 1998 to 2008 and identified all live births with CHD diagnosis (case) and live births without CHD diagnosis (control). We compared prevalence of associated congenital anomalies between the case and control groups. RESULTS Our cohort consisted of 97,154 and 12,078,482 subjects in the case and control groups, respectively. In the CHD population, prevalence of non-syndromic congenital anomaly (NSCA), genetic syndrome (GS), and overall extra-cardiac congenital anomaly (CA) were 11.4, 2.2, and 13.6%, respectively. In the control group, prevalence of NSCA, GS, and CA were 6.7, 0.3, and 7.0%, respectively. NSCA (odds ratio (OR): 1.88, confidence interval (CI): 1.73-1.94), GS (OR 2.52, CI 2.44-2.61), and overall CA (OR: 2.01, CI: 1.97-2.14) were strongly associated with CHD. Prevalence of GS and multiple organ-system CA decreased significantly over the study period. CONCLUSIONS This is the largest and most comprehensive population-based study evaluating association between CHD and extra-cardiac malformation (ECM) in newborns. There was significant decrease in prevalence of GS and multiple CA over the study period.