Considerable numbers of congenital cardiac anomalies are missed at the time of delivery. Study reports show that congenital cardiac anomalies are the second most common birth defect in many countries. Despite this fact, our previous study showed that the prevalence of congenital cardiac anomalies is the fifth most common one, indicating that many of these defects might not be properly diagnosed at the time of delivery and birth. The aim of this study was to estimate the missing frequency of congenital cardiac anomalies at the time of delivery and birth. The population of the study was 185,650 births in the Northwest region of Iran covered by the Tabriz Registry of Congenital Anomalies. A total of 451 children with congenital cardiac anomalies were studied in the region from 2000 to 2009. The expected prevalence of congenital cardiac anomalies at birth was estimated to be 24.2 per 10,000 births while a prevalence of 9.2 per 10,000 births was observed at the same time and place. This indicated that 59.1% of children with congenital cardiac anomalies were not identified at birth (p-value less than 0.05). This proportion increased by 13% over the study period from 2000 to 2009 (p-value greater than 0.1). Our findings indicated that a remarkable frequency of congenital cardiac anomalies was not diagnosed at birth because there was no paediatric cardiologist available at the time of birth in the gynaecology and obstetrics wards.