To assess applicability of noninvasive methods for prenatal sex determination, both intact fetal cells and cell-free DNA from maternal blood were studied. Maternal peripheral blood samples were obtained from 41 women carrying chromosomally normal fetuses and from 3 women with aneuploid fetuses (47,XX,+18; 47,XY,+18 and 47,XY,+21) at 9-22 weeks of gestation. DNA was extracted from the plasma fraction and analyzed by the nested polymerase chain reaction (PCR) using Y chromosome specific primers. After fetal cells were enriched by MACS, fluorescence in situ hybridization (FISH) with chromosome X and Y specific probes was performed to detect XY cells. Although Y-chromosome-specific DNA was detected by PCR analysis in all maternal plasma samples with male fetuses, 26% women bearing female fetuses also gave positive results. By FISH analysis, XY cells were detected in not only 58% of women bearing male fetuses, but also 13% of their counterpoints with female fetuses. Our findings suggested that consistent results for fetal gender using PCR or FISH cannot be obtained with intact fetal cells and cell-free DNA present in maternal blood and plasma at 9-22 weeks of gestation, despite their apparent abundant presence. Copyright 2004 S. Karger AG, Basel