Cell-free fetal DNA can be detected in the blood plasma of pregnant women as early as 5 wk into pregnancy. At present noninvasive prenatal diagnosis has already begun to impact clinical practice. The established applications are for the determination of fetal sex and rhesus D blood group when the mother is rhesus D negative. Both methods are currently evaluated and standardized by a large laboratory network (the Special Non-Invasive Advances in Fetal and Neonatal Evaluation Network, or SAFE) that aims to implement widespread noninvasive prenatal diagnosis throughout the European Union. This chapter presents the basic methodology used in this noninvasive analysis.