Abstract: Objective：To investigate the application of magnetic bead-based DNA extraction technique for the sample preparation of multiplex ligation-dependent probe amplification (MLPA) analysis. Methods：Genomic DNA of peripheral blood samples from 16 healthy male volunteers and a patient with 21-hydroxylase deficiency, as well as amniotic fluid cells from 16 pregnant women was extracted by semiautomatic magnetic bead based DNA extraction method and manual spin column based DNA extraction method. The concentration and purity of DNA samples were compared. The copy numbers of CYP21A2 gene in these samples were determined by MLPA and evaluated. Genomic DNA of amniotic fluid cells from 200 pregnant women was extracted by magnetic bead-based DNA extraction method and the abnormal expressions of chromosomal aneuploidies in the samples were detected by MLPA. Results：Both the concentrations and amounts of genomic DNA extracted from peripheral blood samples by magnetic bead-based DNA extraction were higher than those extracted by spin column based DNA extraction(P<0.05), while the concentrations of DNA extracted from amniotic fluid cells by magnetic bead based method were similar to those extracted by spin column based method. The amounts of genomic DNA extracted from amniotic fluid cells by magnetic bead based DNA extraction method were higher than those extracted by spin column based DNA extraction (P<0.05). The ratio value of copy numbers of CYP21A2 gene in the patient with 21 hydroxylase deficiency was close to 1, which was similar in both extraction by magnetic bead based and spin column based method. Among the 200 samples of amniotic fluid cells, 9 cases of trisomy 21, 2 cases of trisomy 18 and a case of Turner syndrome (45, X) were identified by MLPA, and the other 188 cases were normal diploid. All of these results were concordant with those of karyotyping analysis. Conclusion：The magnetic bead-based DNA extraction method could be used to prepare cellular DNA samples from peripheral blood and amniotic fluid for MLPA analysis.