Objective:To investigate the clinical efficacy of fluorescence in situ hybridization(FISH)in prenatal diagnosis of chromosomal aneuploidy.Methods:FISH and karyotyping analysis were done in 120 samples of amniotic fluid from pregnant women.Results:FISH analysis results were consistent with those of karyotyping,the dectecting rate can reach 100%for chromosomal aneuploidies.There was no significant difference in the preference for FISH or karyotying for prenatal diagnosis when facing high matemal age,multi-indications and other factors(P>0.05).FISH was better when biochemical datafor down's syndrome were positive (P=0.029),however karyotyping was better when there was abnormal fetal ultrasound scan(P=0.000).Conclusions:FISH can detect the chromosomal aneuploidy quickly and accurately,especially when biochemical data for down's syndrome were positive.FISH could be the first choice for prenatal diagnosis in the third trimester of high-risk pregnancy.