Based on genetic and epidemiological studies for the period 2011 – 2018 was compared the frequency, structure and changes over time of rare congenital anomalies (CA) in the population of the Republic of Moldova with the same variables of the International European Register EUROCAT. The study uses an epidemiological approach. Data from the National Register of CA were used for the period 2011 – 2018. Were used statistical data from the official Bureau of Statistics, Republic of Moldova. Materials from the official website of the European Register EUROCAT were used for comparison. CA frequencies were calculated for 1000 newborns. For the monitoring of CA in the Republic of Moldova was developed the National Register of Moldova, formed on the basis of the Laboratory for the Prevention of Hereditary Pathology at the Institute of Mother and Child. Between 2011 and 2018 the mean CA frequency in the population from Republic of Moldova was 17,75 per 1000 newborns, and the same EUROCAT variable was 20,18:1000 newborns, and this variable was subject to fluctuations; so, minimal CA frequency was registered in 2014 (15,38:1000), the maximal value in 2017 (21,84:1000), without the clear trend to increase or decrease. Congenital anomalies do not belongs to rare diseases, as between 2011 and 2018 their average frequency in Moldova was 17,75 per 1000 newborns, and the same value was determined in EUROCAT Register, i. e., 20,18:1000. Analysis of the structure of congenital anomalies during the analyzed period showed that respiratory system anomalies are rare, with a frequency of 0,13:1000 or 1:7692 newborns, meanwhile, in the EUROCAT these CA are 2.6 times more common, but still are a rare anomaly with a frequency of 1:2941. Rare diseases with a frequency exceeding the corresponding EUROCAT indicators include the following congenital anomalies: anencephaly, hydrocephalus, atresia of the anus and of the esophagus, while the frequencies of other rare CA, i. e., omphalocele, reduction of limbs, microcephaly and spina bifida are comparable to similar variables of the European Register.