Introduced by Conrad Hal Waddington in 1942, the concept of epigenetics gave scientists a new paradigm of thought concerning embryonic development, and since then has been widely applied, for instance to inheritable diseases, molecular technologies, and indeed the human genome as a whole. A genome contains an embedded intricate coding template that provides a means of genetic expression from the initial steps of embryonic development until the death of the organism. Within the genome there are two prominent components: coding (exons) and non-coding (introns) sequences. Exons provide coding by transcribing a gene into a protein, while introns do not have this capacity. On top of these coding sequences lie mechanisms that dictate the overall capability of a gene without changing the underlying nucleotide sequence of DNA; these mechanisms are primarily known as epigenetic factors.

In 1914 Albert Niemann, a German pediatrician who primarily studied infant metabolism, published a description of an Ashkenazi Jewish infant with jaundice, nervous system and brain impairments, swollen lymph nodes (lymphadenopathy), and an enlarged liver and spleen (hepatosplenomegaly). He reported that these anatomical disturbances resulted in the premature death of the child at the age of eighteen months. After extensively studying the abnormal characteristics of the infant, Niemann came to the conclusion that the disease was a variant of Gaucher's disease. Gaucher's disease, described by the French dermatologist Philippe Gaucher in 1882, is a lipid storage disorder resulting in an excessive accumulation of lipids in the spleen, kidneys, liver, lungs, bone marrow, and brain. Niemann was able to connect the infant's disease to Gaucher's disease because it displayed similar symptoms: a noticeable accumulation of fatty substances in the brain, liver, and spleen.

Historically the exact age of human embryo specimens has long perplexed embryologists. With the menstrual history of the mother often unknown or not exact, and the premenstrual and postmenstrual phases varying considerably among women, age sometimes came down to a best guess based on the weight and size of the embryo. Wilhelm His was one of the first to write comparative descriptions of human embryos in the late 1800s. Soon afterward, Franklin P. Mall, the first director of the Carnegie Institution of Washington's (CIW) Department of Embryology, expanded upon His' work. Mall's first efforts were to place embryos into stages based on menstrual ages and body length. This method ran into problems however when it became apparent that obtaining menstrual ages was often impossible or simply too inaccurate even if the information could be obtained from the women who carried the embryos. Mall decided instead to look for patterns among embryos to come up with some type of staging system whereby embryo age could be more accurately determined.

Preformationism was a theory of embryological development used in the late seventeenth through the late eighteenth centuries. This theory held that the generation of offspring occurs as a result of an unfolding and growth of preformed parts. There were two competing models of preformationism: the ovism model, in which the location of these preformed parts prior to gestation was the maternal egg, and the spermism model, in which a preformed individual or homunculus was thought to exist in the head of each sperm. Preformationism was a widely-held theory by Enlightenment-era scientists, but by the early 1800s, most scientists had abandoned it, in part because higher magnification in microscopes enabled them to see the very earliest stages of embryos as small collections of cells. Prior to preformationism, naturalists who studied embryo development favored the theory of spontaneous generation in lower animals, such as flies, which appeared to arise from manure. In higher animals, however, scientists used the theory of epigenesis put forth by Aristotle, who said that maternal and paternal fluids came together in the uterus and solidified during early gestation into a fetus. Preformationism was the first theory of generation and development that applied to all organisms in the plant and animal kingdoms.

Fetal programming, or prenatal programming, is a concept that suggests certain events occurring during critical points of pregnancy may cause permanent effects on the fetus and the infant long after birth. The concept of fetal programming stemmed from the fetal origins hypothesis, also known as Barker’s hypothesis, that David Barker proposed in 1995 at the University of Southampton in Southampton, England. The fetal origins hypothesis states that undernutrition in the womb during middle to late pregnancy causes improper fetal growth, which in turn, causes a predisposition to certain diseases in adulthood. In addition to nutritional impacts, researchers have studied the fetal programming effects of many factors, such as maternal anxiety or violence during pregnancy. Researchers proposing the concept of fetal programming established a new area of research into the developmental causes of disease, pointing towards the in utero environment and its critical role in healthy human development.

Endoderm is one of the germ layers-- aggregates of cells that organize early during embryonic life and from which all organs and tissues develop. All animals, with the exception of sponges, form either two or three germ layers through a process known as gastrulation. During gastrulation, a ball of cells transforms into a two-layered embryo made of an inner layer of endoderm and an outer layer of ectoderm. In more complex organisms, like vertebrates, these two primary germ layers interact to give rise to a third germ layer, called mesoderm. Regardless of the presence of two or three layers, endoderm is always the inner-most layer. Endoderm forms the epithelium-- a type of tissue in which the cells are tightly linked together to form sheets-- that lines the primitive gut. From this epithelial lining of the primitive gut, organs like the digestive tract, liver, pancreas, and lungs develop.

The sex of a reptile embryo partly results from the production of sex hormones during development, and one process to produce those hormones depends on the temperature of the embryo's environment. The production of sex hormones can result solely from genetics or from genetics in combination with the influence of environmental factors. In genotypic sex determination, also called genetic or chromosomal sex determination, an organism's genes determine which hormones are produced. Non-genetic sex determination occurs when the sex of an organism can be altered during a sensitive period of development due to external factors such as temperature, humidity, or social interactions. Temperature-dependent sex determination (TSD), where the temperature of the embryo's environment influences its sex development, is a widespread non-genetic process of sex determination among vertebrates, including reptiles. All crocodilians, most turtles, many fish, and some lizards exhibit TSD.

Wilhelm Johannsen in Denmark first proposed the distinction between genotype and phenotype in the study of heredity in 1909. This distinction is between the hereditary dispositions of organisms (their genotypes) and the ways in which those dispositions manifest themselves in the physical characteristics of those organisms (their phenotypes). This distinction was an outgrowth of Johannsen's experiments concerning heritable variation in plants, and it influenced his pure line theory of heredity. While the meaning and significance of the genotype-phenotype distinction has been a topic of debate-among Johannsen's contemporaries, later biological theorists, and historians of science-many consider the distinction one of the conceptual pillars of twentieth century genetics. Moreover some have used it to characterize the relationships between studies of development, genetics, and evolution.

Tooth enamel contains relics of its formation process, in the form of microstructures, which indicate the incremental way in which it forms. These microstructures, called cross-striations and striae of Retzius, develop as enamel-forming cells called ameloblasts, whcih cyclically deposit enamel on developing teeth in accordance with two different biological clocks. Cross-striations result from a twenty-four hour cycle, called a Circadian rhythm, in the enamel deposition process, while striae of Retzius have a longer periodicity. Unlike other tissues, enamel does not remodel after it forms, leaving those microstructures intact after deposition. Cross-striations and striae of Retzius thus provide evidence of the timing and processes of tooth development, and they indicate how organisms in a lineage differently grow and develop across generations. Researchers have examined those microstructures to investigate human evolution.

In 1868 in England, Charles Darwin proposed his pangenesis theory to describe the units of inheritance between parents and offspring and the processes by which those units control development in offspring. Darwin coined the concept of gemmules, which he said referred to hypothesized minute particles of inheritance thrown off by all cells of the body. The theory suggested that an organism's environment could modify the gemmules in any parts of the body, and that these modified gemmules would congregate in the reproductive organs of parents to be passed on to their offspring. Darwin's theory of pangenesis gradually lost popularity in the 1890s when biologists increasingly abandoned the theory of inheritance of acquired characteristics (IAC), on which the pangenesis theory partially relied. Around the turn of the twentieth century, biologists replaced the theory of pangenesis with germ plasm theory and then with chromosomal theories of inheritance, and they replaced the concept of gemmules with that of genes.