Timely detection of fetal aneuploidy is an important aspect of clinical practice. At present, analytical techniques involving high-throughput sequencing are on the rise. Noninvasive prenatal testing (NIPT) ensures reliable results as early as week 9–11 into pregnancy. This article describes a clinical case of NIPT application and further verification of its results. Using next-generation sequencing, the microarray analysis of cell-free DNA in the amniotic fluid and the cytogenetic analysis of fetal chromosomes, a high risk of chromosomal rearrangements was detected in the short arms of chromosomes 4 and 12. This prediction was verified by molecular karyotyping conducted in both parents. The mother was found to be a balanced carrier of translocations between chromosomes 4 and 12. This case demonstrates the advantages of a whole-genome approach to NIPT over targeted-based.