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Abstract Background 22q11.2 deletion syndrome (22q11.2DS) and 22q11.2 duplication syndrome (22q11.2DupS) are the most common copy number variations in humans. The clinical phenotypes of these two syndromes are variable, and there are no large sample data on the prenatal detection rate for these two syndromes in the Chinese population. Results We recruited 411 pregnant women who showed either abnormal prenatal ultrasound findings or positive prenatal BoBs™ results or who had given birth to a child with chromosomal abnormalities. SNP-array analysis and interphase FISH analysis identified five fetuses with 22q11.2 copy number variants (CNVs), three of which were 22q11.2 deletion syndrome (22q11.2DS) (3/411) and two of which were 22q11.2 duplication syndrome (22q11.2DupS). In all 5 cases of diagnosed 22q11.2 abnormalities, inheritance could not be identified because the parents did not undergo further testing. Conclusion Our case reports provide a detection rate of 22q11.2 CNVs for fetuses with prenatal diagnostic indications, and early diagnosis of these two syndromes was essential for prenatal intervention in these cases. SNP-array technology is an effective tool in the prenatal diagnosis of 22q11.2 CNVs. The prenatal diagnosis of these two syndromes is helpful for early intervention, which is of great clinical significance.