There is a great effort to find out the biological role of cell-free nucleic acids (cfNAs). They are considered very promising targets in the diagnosis of genetic diseases. Non-invasive sampling (liquid biopsy) has recently become a very popular method, and new molecular biological techniques have been developed for these types of samples. Application of next-generation sequencing (NGS) and massively parallel sequencing (MPS) is spreading fast. These are the part of the arsenal of the modern prenatal genetic diagnostic laboratories by now. Cell-free DNA based noninvasive prenatal testing accounts for more than half of the prenatal genetic tests performed, it is gradually replacing the invasive amniocentesis or chorionic villus sample-based diagnostics. Besides that, new non-coding RNAs are taking more attention: microRNAs (miRNAs), long non-coding RNAs (lncRNAs), circular RNAs (circRNAs) are in the focus of the clinical research to detect the most common pregnancy-associated diseases, like preeclampsia, fetal growth restriction, congenital heart diseases and gestational diabetes. The research is at advanced stage on the use of microRNAs, while lncRNAs and circRNAs are still promising targets. In this review, comprehensive information is given about the recent developments on this field.