Objectives: This study was conducted to determine the prevalence of chromosomal anomalies in newborns with structural heart disease admitted to the cardiac intensive care unit (CICU) at Nicklaus Children's Hospital (NCH). Methods: A retrospective review identified newborns age 30 days or less admitted to NCH CICU between 2004 and 2010. Patients with structural heart disease who required admission to our CICU and received karyotype or karyotype and fluorescent in situ hybridization (FISH) testing were included in the study. All patients were examined for the presence of dysmorphic features. Results: Four hundred and eighty-two patients met the criteria for the study; 405 (84%) received both karyotype and FISH. Chromosome abnormalities were present in 86 (17.8%) patients. Syndromes accounted for 20 (5.1%) of those with normal chromosomes. Dysmorphic features were seen in 79.1% of patients with abnormal chromosomes and 25.5% of those with normal chromosomes. All patients with syndromes were dysmorphic. Race and gender did not significantly affect the incidence of genetic abnormalities. Conclusions: Chromosome abnormalities, including syndromes, are prevalent in newborns with congenital heart disease. Further research is needed to evaluate the utility of cytogenetic screening in all children with congenital heart disease.