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Introduction. Multiplex Ligation-dependent Probe Amplification (MLPA) and Quantitative Fluorescent- Polymerase Chain Reaction (QF-PCR) techniques were reported to be efficient without conventional karyotyping for prenatal diagnosis of aneuploidies. However, there are a lot of situations where QF-PCR and MLPA techniques may miss out some genetic abnormities. For example, the mosaicism is an interesting situation. In order to evaluate and to compare the level of chromosomal mosaicism detection by QF-PCR and MLPA techniques in prenatal diagnosis of fetal aneuploidies, we conducted the present experimental study. Materials and method. The DNA of a 17-month-old fetus diagnosed with complete trisomy 21 was used for MLPA analysis. The DNA with complete trisomy 21 was diluted with a DNA without aneuploidies (the control DNA). For QF-PCR we included one probe, confirmed by conventional karyotyping, with trisomy 21 (with a translocation) in 50% of the cells. In this respect, SALSA MLPA P095 Aneuploidy and Elucigene QST*R Plusv2 kits were used. Results. The MLPA analysis was able to confirm the diagnosis of trisomy 21 on probes with mosaicism (with 50% of cells with trisomy) and also to suggest the possibility of trisomy in cases with 25% mosaicism. The QF-PCR technique was unable to detect the genetic anomaly of the probe used. Each technique, including the conventional karyotyping, has several advantages, disadvantages and challenges that will be discussed, including the costs of each analysis. Conclusions. Based on our results, MLPA analysis seems to be more efficient on mosaicism detection. The QF-PCR had the advantage of DNA contamination detection which also is very important on prenatal diagnosis. [ABSTRACT FROM AUTHOR]