Extracardiac or genetic abnormalities (EGA) represent a factor in the morbidity of patients with congenital heart disease. We evaluated the way neonates with CHD are screened at our institution and determined the yield for the screening tests. We reviewed the charts of 223 neonates with structural CHD. Subjects were categorized into 6 groups: univentricular, left-sided obstructive lesions, right-sided obstructive lesions, septal defects, conotruncal defects (CTD), and other. We reviewed which patients underwent cranial ultrasonogram (CUS), abdominal ultrasonogram (AUS), and/or genetic studies (GS) as well as their results. There was a high prevalence of EGA in each group by CUS (32% to 42%), AUS (32% to 69%), and GS (10% to 60%). There was considerable variability in the proportion within each group that underwent screening tests, and the consistency of screening often was not congruent with the likelihood of abnormal results. Approximately 50% of our patients had >/=1 EGA identified, resulting in a cost-yield ratio of $4,508/patient with EGA. Screening for EGA at our institution is not uniform and is often at odds with the prevalence of such patients. Given the high prevalence of EGA, we advocate for a universal screening program for neonates with CHD using cranial/abdominal ultrasonography and genetic testing.