The discovery of circulating fetal DNA paves a new way for non-invasive prenatal diagnosis. Examining the specific fetal DNA sequence of the circulating fetal DNA has been used for prenatal diagnosis of sex-linked disorders, fetal rhesus D blood typing and single gene inheritance disease. The variation of the circulating DNA levels can also be used for diagnosis of preeclampsia, premature delivery, and fetal chromosome disorders. This paper aims to review the biochemistry characters and clinical application of the circulating fetal DNA in maternal peripheral plasma.