Congenital malformations, chromosomal and monogenic disease play a significant role in perinatal mortality and child disability. According to the early prenatal screening results in the Russian Federation in 2018, the overall ratio of chromosomal anomaly prevalence is 1:250–1:300. Currently aneuploidy risk is calculated by using indirect biochemical and ultrasound markers, that have low sensitivity and specificity which can cause false positives and false negative results leading to unreasonable invasive procedures or missing chromosomal anomalies. It is well known that cell-free fetal DNA is detected in maternal blood. Whole‐genome sequencing based non-invasive prenatal testing (NIPT) can detect fetal chromosomal aneuploidy with high sensitivity as early as 10 weeks into pregnancy. The accuracy of determining fetal sex is also high: sensitivity and specificity are 98,9% and 99,9% respectively. Implementing molecular technology into clinical practice is required to improve prenatal diagnosis in the Russian Federation, icluding Moscow. Integration of NIPT to analyse cell-free fetal DNA will increase the efficiency of fetal chromosomal anomalies’ detection. However, there are some legal and ethical aspects to consider when integrating a new technology for wide-spread use. This review reveals arguable issues of NIPT integration into widespread clinical practice and possible ways of solving those issues. Key words: NIPT, noninvasive prenatal test, prenatal screening, fetal sex, invasive prenatal diagnosis, X-linked disease, chromosomal anomaly, chromosomal microarray analysis