Objective <p>Assessment of the clinical utility of combined karyotyping and CNV-seq for detecting sex chromosome and autosomal mosaicism in amniotic fluid.</p> Methods <p>A retrospective analysis was conducted on the data of 3307 pregnant women who underwent both amniotic fluid chromosome karyotyping and CNV-seq testing.</p> Results <p>The two techniques collectively detected 66 cases of mosaicism, with a detection rate of 2.00%. The concordance rate between the two techniques was 43.94% (29/66). The concordance rate for sex chromosome mosaicism was 77.78% (21/27), while it was 20.51% (8/39) for autosomal mosaicism. Among the 27 cases of sex chromosome mosaicism, 11 opted to continue the pregnancy and delivered infants with no apparent abnormalities. In one of these cases, the karyotype was suspected to be pseudomosaicism (mosaicism was found in only one cell line of the karyotype analysis), and the newborn’s peripheral blood chromosome karyotype revealed low-level mosaicism.</p> Conclusion <p>The combined use of karyotyping and CNV-seq enhances the detection capability for low-percentage sex chromosome mosaicism in amniotic fluid. In cases of discordant results between these methods, fluorescence in situ hybridization (FISH) is recommended for confirmation. Furthermore, the clinical management of any identified low-level mosaicism should be integrated with comprehensive genetic counseling.</p>