Fluorescence in situ hybridization (FISH) in uncultured amniotic fluid samples is a useful tool for rapid prenatal diagnosis in pregnancy with high risk for chromosomal aneuploidy. FISH using specific probes for chromosome 21 was performed in 39 amniotic fluid samples referred to the Institute of Reproductive Medicine and Population, Seoul National University. The results of FISH analysis were compared to the karyotype using conventional cytogenetic analysis. The most frequent indication performed FISH analysis was the abnormal ultrasonographic findings (61.5%). Trisomy 21 was identified in two our of 39 uncultured amniotic fluid samples by FISH. Conventional cytogenetic results revealed four chromosomal abnormalities which were not detectable by targeted FISH of chromosome 21 such as trisomy 13 and 18, inversion 5 and balanced reciprocal translocation. Interphase FISH analysis would be effective in conjunction with the conventional cytogenetic analysis.