Background: Congenital heart diseases affect a large number of newborns and account for a high proportion of infant mortality worldwide. There are regional differences in the prevalence and distribution pattern of congenital heart diseases. We aimed to evaluate the relative frequencies, risk factors and diagnostic clues of congenital heart disease in newborns at our neonatal intensive care unit. Materials and methods: Among 326 cases admitted to the Abant Izzet Baysal University Neonatal Intensive Care Unit between February 2013 - September 2014, thirty-five newborns with congenital heart disease were evaluated, retrospectively. Data was collected on a predesigned proforma containing information regarding gender, gestational age and weight at birth, family history, and associated malformations. Results: The prevalence of congenital heart disease was 10.7%. The most common cause for cardiology consultation was cardiac murmur (85.5%). The relative percentage of acyanotic and cyanotic heart defects were 91.6% and 8.4%, respectively. The most frequent acyanotic defect was ventricular septal defect with a prevalence of 22.8%. Maternal diabetes mellitus and Down syndrome were observed in 17.1% and 2.8% of cases, respectively. Conclusion: The prevalence of congenital heart disease in newborns at the neonatal intensive care unit was higher than that in all live births and most common defect was muscular VSD. The most frequent diagnostic clue was cardiac murmur.