Exposure to environmental contaminants during the critical window of pregnancy results in deregulation of highly coordinated genetic and epigenetic mechanisms involved in prenatal growth. Such disturbances significantly alter the fetal programming, and lead to various developmental disorders immediately, over the lifetime, or transgenerationally. During the process of placental development, fetal nucleic acids enter maternal plasma as a result of necrotic, apoptotic, and inflammatory mechanisms. These nucleic acids reflect normal or abnormal ongoing cellular changes during prenatal fetal development. Here, we critically review the utility of maternally circulating cell free fetal nucleic acids towards developing reliable biomarkers for widespread screening of environmentally-associated fetal abnormalities. We further discuss the most recent developments in the fetal nucleic acid analysis, quantification methodologies, challenges involved in their accurate detection and their potential applications in fetomaternal medicine.