Background Trisomy 21 is the most common chromosomal aberration in live births. Some efforts have been made to develop noninvasive prenatal detection of trisomy 21 by using fetal DNA in maternal plasma. Due to the maternal DNA background, a distinguishable marker between maternal DNA and fetal DNA must be used, such as DNA methylation. The objective of this study was to search for fetal-specific methylation markers on chromosome 21. Methods We chose six genes highly or specifically expressed in placenta and screened the methylation status of these gene promoter regions by combination of methylated-DNA precipitation and methylation-sensitive restriction enzymes assay (COMPARE-MS). We further determined the methylation status of each CpG site within selected gene fragments by bisulfite sequencing. At last, we detected the placenta-derived methylation marker in the first-trimester maternal plasma by real-time methylation-specific PCR (MSP). Results Down syndrome (DS) critical region gene 4 (DSCR4) promoter region was found to be hypomethylated in placental tissues and densely methylated in maternal blood cells. Unmethylated DSCR4 (Down syndrome) sequence can be detected in the first-trimester maternal plasma. Conclusion DSCR4 promoter DNA is a candidate fetal epigenetic marker for noninvasive prenatal detection of trisomy 21. Copyright  2011 John Wiley & Sons, Ltd.