AbstractObjectiveOligonucleotide‐based array comparative genomic hybridization (array CGH) is an established method for detecting chromosomal abnormalities. Here, we explored the feasibility of using DNA extracted from uncultured amniocytes in amniotic fluid for array CGH on an oligonucleotide array platform.MethodsFifteen fetuses from 14 ongoing pregnancies were studied by array CGH on targeted oligonucleotide arrays with DNA isolated from direct amniotic fluid using a modified DNA extraction protocol.ResultsHigh‐quality array CGH results were obtained for 13 samples with suboptimal but interpretable results in only 2 samples due to limited DNA amounts. Array CGH using whole genome amplification (WGA) of DNA for the two cases with limited DNA was successful, and results were consistent with those from unamplified DNA. For another five samples, the results of array CGH with amplified DNA matched those with unamplified DNA. Chromosome analysis was performed for 14 cases and was consistent with array CGH results.ConclusionThis study demonstrates the feasibility of prenatal genetic diagnosis using oligonucleotide array CGH analysis for direct analysis of amniocytes without culturing cells. The use of oligonucleotide arrays increases the sensitivity and accuracy of detection over previous bacterial artificial chromosome (BAC)‐based arrays. Furthermore, the direct analysis allows for rapid array CGH results and shorter reporting time. Copyright © 2008 John Wiley & Sons, Ltd.