In Estonia invasive prenatal diagnosis was introduced into clinical practice in spring 1990. Altogether 22342 invasive procedures were done: 21150 amniocentese, 1139 chorionic villus samplings, and 53 cordocentese. Chromosomal abnormalities were detected in 1026 (4.6%) cases, 74% of them were numerical changes. The most common diagnosis (n = 435) was trisomy 21 (Down syndrome). Monogenic diseases were diagnosed in 35 cases. The main indication for invasive procedures is currently positive serum screening result, followed by abnormal ultrasound finding. Screening for chromosomal abnormalities (mainly Down syndrome) for advanced maternal age (>35/37) started in Estonia in 1995 and maternal serum creening (double/ triple test) for women <35 was introduced in autumn 1998. In 2013, 98% pregnant women in Estonia were monitored. During the period 1995–2016, 64% of DC were diagnosed prenatally. The incidence of DS after implementation of prenatal screening in Estonia has decreased.