Abstract: Objective To apply chromosomal microarray analysis (CMA) in the diagnosis of karyotyping with uncertain genomic rearrangement. Methods We retrospectively reviewed 48 samples （34 samples of amniotic fluid，14 samples of peripheral blood） of karyotype analyses with uncertain genomic rearrangement in patients admitted to our department from September 2014 to April 2016. The CMA results were compared with those of karyotyping. Results The 48 samples consisted of 13 samples with marker chromosomes, 19 samples with derivative chromosomes, and 16 samples with balanced translocation. Sixteen cases (33.33%) were detected with abnormalities by CMA. In the 32 samples with marker chromosomes or derivative chromosomes, 16 cases were detected with deletions or duplications (>5 Mb) by CMA, including 1 case 21-trisomy, 2 cases XYY syndrome and 3 cases microdeletion/ microduplication syndromes (22q11 duplication syndrome, Wolf-Hirschhorn syndrome and 15q26 overgrowth syndrome). In the 16 balanced translocation cases, all revealed negative results in CMA. Conclusion CMA can confirm the karyotyping with uncertain genomic rearrangement and clarify its clinical significance.