Congenital rubella syndrome (CRS) can occur in children whose mothers contracted the rubella virus, sometimes called German measles, during pregnancy. Depending on the gestational period when the mother contracts rubella, an infant born with CRS may be unaffected by the virus or it may have severe developmental defects. The most severe effects of the virus on fetal development occur when the mother contracts rubella between conception and the first trimester. Defects from maternal rubella in the first trimester are included in the term congenital rubella syndrome, but physicians and researchers specifically refer to those defects as rubella embryopathy. Developmental defects are less severe if the mother contracts rubella in the second trimester, and they are generally negligible if the infection occurs in the third trimester. Prenatal rubella infection can cause birth defects which include deafness, compromised vision, abnormal heart development, and damage to the central nervous system which can lead to compromised cognition and learning disabilities.

In his 1991 article Screening for Congenital Hypothyroidism, Delbert A. Fisher in the US reported on the implementation and impact of mass neonatal screening programs for congenital hypothyroidism (CH) from the early 1970s through 1991. CH is a condition that causes stunted mental and physical development in newborns unless treatment begins within the first three months of the newborn's life. In the early 1970s, regions in Canada and the US had implemented screening programs to diagnose and treat CH as quickly as possible after the infant's birth. By 1991 many other countries had adopted the early screening program, and Fisher estimated that 10 to 12 million newborns per year were tested in the early 1990s. The screening programs, along with physician education and improved screening techniques, such as radioimmunoassay, helped significantly reduce the incidence of abnormal newborn development resulting from untreated congenital hypothyroidism.

In Australia in the 1940s, Norman McAlister Gregg observed a connection between pregnant women who contracted the rubella virus, or German measles, and cataract formation in their children's eyes. Gregg published his findings in the 1941 article Congenital Cataract following German Measles in the Mother in Transactions of the Ophthalmological Society of Australia. In the article, Gregg analyzed seventy-eight cases of congenital cataracts and suggested that the mothers' environmental factors could cause birth defects, otherwise known as teratogenic effects. Gregg's paper on the teratogenic effects of an environmental agent, the rubella virus, changed the study of birth defects to include viruses as potential causes or teratogens.

Fetal surgeries are a range of medical interventions performed in utero on the developing fetus of a pregnant woman to treat a number of congenital abnormalities. The first documented fetal surgical procedure occurred in 1963 in Auckland, New Zealand when A. William Liley treated fetal hemolytic anemia, or Rh disease, with a blood transfusion. Three surgical techniques comprise many fetal surgeries: hysterotomy, or open abdominal surgery performed on the woman; fetoscopy, for which doctors use a fiber-optic endoscope to view and make repairs to abnormalities in the fetus; and percutaneous fetal theray, for which doctors use a catheter to drain excess fluid. As the sophistication of surgical and neonatal technology advanced in the late twentieth century, so too did the number of congenital disorders fetal surgeons treated, such as mylomeningeocele, blocked urinary tracts, twin-to-twin transfusion syndrome, polyhydramnios, diaphragmatic hernia, tracheal occlusion, and other anomalies. Many discuss the ethics of fetal surgery, as many consider it contentious, as fetal surgery risks both the developing fetus and the pregnant woman, and at times it only marginally improves patient outcomes. Some argue, however, that as more advanced diagnostic equipment and surgical methods improve, advanced clinical trials in a few conditions may demonstrate more benefits than risks to both pregnant women and fetuses.

Anencephaly is an open neural tube defect, meaning that part of the neural tube does not properly close or that it has reopened during early embryogenesis. An embryo with anencephaly develops without the top of the skull, but retains a partial skull, including the face. Anencephaly is one of the most common birth defects of the neural tube, occurring at a rate of approximately one in one thousand human pregnancies. The condition can be caused by environmental exposure to chemicals, dietary deficiencies, or genetic mutations.

Johann Friedrich Meckel and Antoine Etienne Reynaud Augustin Serres developed in the early 1800s the basic principles of what later became called the Meckel-Serres Law. Meckel and Serres both argued that fetal deformities result when development prematurely stops, and they argued that these arrests characterized lower life forms, through which higher order organisms progress during normal development. The concept that the embryos of higher order organisms progress through successive stages in which they resemble lower level forms is called recapitulation. Meckel, a professor of anatomy at the University of Halle in Halle, Germany, and Serres, a physician at Hotel-Dieu de Paris in Paris, France, did not work together. Rather, in the late nineteenth and early twentieth centuries, their similar approaches, in which they compared the anatomy and embryos of different species so as to relate stages of embryonic development to the scala naturae, led oher scientists to generalize their individual concepts into one general theory. The recapitulation ideas of Meckel and Serres became part of the mid-eighteenth century debate about how to explain morphological similarities between species.

Surgeons sometimes operate on the developing fetuses in utero of pregnant women as a medical intervention to treat a number of congential abnormalities, operations that have ethical aspects. A. William Liley performed the first successful fetal surgery, a blood transfusion, in New Zealand in 1963 to counteract the effects of hemolytic anemia, or Rh disease. The ethical discussions surrounding fetal surgery are complex and are still being defined, as fetal surgery represents an emerging field of in utero medical interventions that impact the quality of life for both pregnant women and fetuses. Such discussions involve the ethical relationships between parents, fetuses, doctors, and health care organizations like hospitals. What may benefit the fetus may harm the pregnant woman, and what may benefit the pregnant woman could negatively impact the viability of the pregnancy. Risks to the pregnant woman include preterm membrane rupture, preterm labor, wound infection, hemorrhage, loss of uterus, damage to the organs near the uterus, and possibly death. Fetal surgery does not always improve the quality of life for the developing fetus, and the risks and benefits of fetal surgery must be carefully weighed and discussed between the medical team, the pregnant woman, and her partner to customize the most ethical plan of action

In 1616 in Padua, Italy, Fortunio Liceti, a professor of natural philosophy and medicine, wrote and published the first edition of De Monstruorum Causis, Natura et Differentiis (On the Reasons, Nature, and Differences of Monsters), hereafter De monstruorum. In De monstruorum, Liceti chronologically documented cases of human and animal monsters from antiquity to the seventeenth century. During the seventeenth century, many people considered such monsters as frightening signs of evil cursed by spiritual or supernatural entities. Liceti categorized monsters based on their potential causes, several of which he claimed were unrelated to the supernatural. Historians later noted that some documented monsters were infants with birth defects. In De monstruorum, Liceti elevated the status of monsters to potential subjects of scientific inquiry and provided an early model for the study of birth defects, a field later called teratology.

Fetus in fetu is a rare variety of parasitic twins , where the developmentally abnormal parasitic twin is completely encapsulated within the torso of the otherwise normally developed host twin. In the late eighteenth century, German anatomist Johann Friedrich Meckel was the first to described fetus in fetu, which translates to “fetus within fetus.” Fetus in fetu is thought to result from the unequal division of the totipotent inner cell mass , the mass of cells that is the ancestral precursor to all cells in the body. The unequal division is thought to occur during the formation of the blastocyst, which can also result in parasitic and conjoined twins . Fetus in fetu represents a developmental anomaly that has prompted developmental biologists to further examine the mechanisms for how twins arise.

Fortunio Liceti studied natural philosophy and medicine in Italy during the first half of the seventeenth century. Liceti wrote greater than seventy works on a wide range of topics, including the human soul, reproduction, and birth defects observed in animals and human infants. In the seventeenth century, people commonly addressed birth defects using superstition and considered them as signs of evil, possibly caused by spiritual or supernatural entities. Liceti described infants with birth defects as prodigies and monsters to be admired and studied rather than feared. Liceti’s works established monsters as a possible subject of scientific inquiry and served as models for the future study of birth defects, a field later called teratology. Liceti was one of the first scholars to attempt to systematically categorize birth defects based on their causes, including multiple causes unrelated to the supernatural.