Prenatal genetic counseling is a communication process to help in decision making during or before a pregnancy, which deals with the inheritance patterns, carrier frequencies, recurrence risks, available genetic tests, and potential management options of a genetic disorder in a family. The ethical and technical challenges are significant in the area of prenatal medicine as the fetus has a relatively short medical history, and the morphological assessment is only feasible indirectly through ultrasound. Fetal DNA can be obtained either directly from placental biopsy or amniotic fluid, or indirectly through cell-free fetal DNA circulating in the maternal plasma. For a group of fetal malformations diagnosed during ultrasound evaluation, there is inadequate information to establish a definite diagnosis, and inquiries about the pathogenesis of the fetal abnormalities and their recurrence may be delineated only after postnatal or pathological examination. Uncertainty in diagnosis and prognosis is challenging for physicians and distressing for families. The introduction of chromosomal microarray into the field of fetal medicine has dramatically increased the diagnostic yield of diagnostic tests in several scenarios, including cases of nonimmune hydrops fetalis, and multiple congenital anomalies. New fetal phenotypes evolved by whole-exome sequencing pose a major challenge during pregnancy as the malformations may not yet have manifested during the gestational period when the fetus is assessed. Large-scale efforts to create public databases of whole-exome sequencing findings and their associated fetal phenotypes will greatly enhance counseling abilities. Finally, the increase in use of preimplantation genetic diagnosis poses numerous social, psychological, ethical, clinical, and legal dilemmas, many of which have received little attention.