Rapid molecular biological methods (FISH, QF-PCR, MLPA, MAPH, quantitative real-time PCR, melting analysis of SNP, etc.) for prenatal diagnosis of the most common aneuploidies are not used so far as stand-alone tests. However some of them are now routinely applied as a preliminary test. That shortens the waiting time for classic cytogenetics analysis and relieves the anxiety levels in pregnant women. Here we report our background with the QF-PCR technique. A total of 1476 prenatal DNA samples extracted from amniotic fluid cells, chorionic villi and fetal tissue after abortions were analyzed. Ten STR markers on chromosomes 13, 18 and 21 were used in multiplex assays. All of the samples with numerical chromosomal anomalies, concerning target chromosomes were correctly diagnosed with QF-PCR technique. Thirteen samples were with sex chromosome aneuploidies and 6 samples had karyotypes with structural chromosomal anomalies on other chromosomes not included in our analysis. Our experience showed that QF-PCR technique could be used for detection of certain chromosomal numerical anomalies. The choice of molecular method for the detection of aneuploidy should depend on the indications for the test. In low-risk patients the use of molecular methods as the only method of diagnosis and testing only for the most common autosomal aneuploidies could be acceptable, especially in small countries with limited resources. However for pregnancies with a high risk of aneuploidies because of suspicious ultrasound screening or family history for balanced karyotype rearrangements, a more detailed analysis as karyotyping is appropriate.