Hilde Mangold, previously Hilde Proescholdt, was a German embryologist and physiologist who became well known for research completed with Hans Spemann in the 1920s. As a graduate student, Mangold assisted Spemann and together they discovered and coined the term the "organizer." The organizer discovery was a crucial contribution to embryology that led to further understanding of the pattern of embryo differentiation of amphibians. Mangold's dissertation was connected to Spemann's Nobel Prize, but Mangold died early in life and was unable to witness the impact her research had on experimental embryology.

The Notch signaling pathway is a mechanism in animals by which adjacent cells communicate with each other, conveying spatial information and genetic instructions for the animal's development. All multicellular animals utilize Notch signaling, which contributes to the formation, growth, and development of embryos (embryogenesis). Notch signaling also contributes to the differentiation of embryonic cells into various types of cells into various types of cells, such as neurons. Research into the Notch gene in fruit flies began in the early twentieth century, but not until the end of the twentieth century did researchers begin to uncover, in many different species, the roles of Notch proteins for cell to cell signaling. Researchers have also found that dysfunction in the pathway can contribute to diseases such as cancer and Alzheimer's.

Among other functions, the Notch signaling pathway forestalls the process of myogenesis in animals. The Notch signaling pathway is a pathway in animals by which two adjacent cells within an organism use a protein named Notch to mechanically interact with each other. Myogenesis is the formation of muscle that occurs throughout an animal's development, from embryo to the end of life. The cellular precursors of skeletal muscle originate in somites that form along the dorsal side of the organism. The Notch signaling pathway is active in multiple aspects of somitogenesis, and it continues to be a critical regulator during myogenesis. Throughout the life of an organism, Notch signaling prevents the differentiation of muscle progenitor cells into muscle cells. Such preventions help maintain populations of progenitor cells that can remain dormant until the growth or repair of muscle is necessary, at which point the Notch signal to the muscle progenitor cells is disrupted, and the muscle progenitor cells differentiate into muscle fibers and cells. Without Notch signaling, myogenesis proceeds prematurely and dissipates before mature muscle can form.

Conrad Hal Waddington's Organisers and Genes, published in 1940, is a summary of available research and theoretical framework for many concepts related to tissue differentiation in the developing embryo. The book is composed of two main conceptual sections. The first section explores the action and nature of the organizer, while the second section delves into genes and their influence on development.

Between February 1969 and August 1970 Edward Kollar and Grace Baird, from the University of Chicago in Chicago, Illinois, published three papers that established the role of the mesenchyme in tooth induction. Drawing upon a history of using tissue interactions to understand differentiation, Kollar and Baird designed their experiments to understand how differentiated structures become specified. Their work overturned a widely accepted model that epithelium controls the identity of the structure, a phenomenon called structural specificity. Interactions between epithelium and mesenchyme control the development and differentiation of many parts during embryonic development, including structures like the gastrointestinal tract and hair. Thus, the realization that mesenchyme drives induction and differentiation during epithelio-mesenchymal interactions had far-reaching effects.

Stem cells are undifferentiated cells that are capable of dividing for long periods of time and can give rise to specialized cells under particular conditions. Embryonic stem cells are a particular type of stem cell derived from embryos. According to US National Institutes of Health (NIH), in humans, the term "embryo" applies to a fertilized egg from the beginning of division up to the end of the eighth week of gestation, when the embryo becomes a fetus. Between fertilization and the eighth week of gestation, the embryo undergoes multiple cell divisions. At the eight-cell stage, roughly the third day of division, all eight cells are considered totipotent, which means the cell has the capability of becoming a fully developed human being. By day four, cells begin to separate and form a spherical layer which eventually becomes the placenta and tissue that support the development of the future fetus. A mass of about thirty cells, called the inner cell mass, forms at one end of the sphere and eventually becomes the body. When the sphere and inner cell mass are fully formed, around day 5, the pre-implantation embryo is referred to as a blastocyst. At this point the cells in the inner cell mass have not yet differentiated, but have the ability to develop into any specialized cell type that makes up the body. This property is known as pluripotency. As of 2009, embryonic stem cells refer to pluripotent cells that are generally derived from the inner cell mass of blastocysts.

Charles Manning Child designed an experimental test, the susceptibility assay, to measure the effects of different toxins on developmental processes. The susceptibility assay measured an organism s vulnerability to death when it was submerged in a noxious solution. The assay involved immersing an organism in a solution that contained a depressant or inhibitory substance, such as alcohol, and then measuring the responses of the organism. Child interpreted these measurements as revealing information about the relative levels of metabolic activity within the organism. Child predicted an organism's susceptibility to death should vary directly with its metabolic rate. An organism with a high metabolic rate would be expected to die more quickly in a noxious chemical solution than an organism with a lower metabolic rate: the higher the rate, the more quickly death should ensue. He also predicted young organisms should have higher metabolic rates than older organism, since children were known to metabolize drugs more quickly than adults.

The term morphogenesis generally refers to the processes by which order is created in the developing organism. This order is achieved as differentiated cells carefully organize into tissues, organs, organ systems, and ultimately the organism as a whole. Questions centered on morphogenesis have aimed to uncover the mechanisms responsible for this organization, and developmental biology textbooks have identified morphogenesis as one of the main challenges in the field. The concept of morphogenesis is intertwined with those of differentiation, growth, and reproduction. Each comprises the fundamental components of development that have commonly been used to categorize the problems that motivate developmental biology.

Research in chemical induction seeks to identify the compound or compounds responsible for differentiation in a developing embryo. Soren Lovtrup compared the search for these compounds to the search for the philosopher's stone. It was based on the assumption that the differentiating agents have to be chemical substances either within cells or in the extracellular matrix. However, despite numerous efforts to understand them, the nature of these substances remained largely a mystery from the 1930s until the 1980s, when the new era of molecular induction based on molecular genetics provided a new perspective. During the period of emphasis on chemical induction, a variety of different experiments were conducted aimed at discovering the chemical nature of the inducer. In some experiments, the organizer region was killed by heat to assess the inducing ability of a dead organizer. Other experiments used natural and synthetic compounds to attempt. Although none of these experiments identified a chemical inducer with any certainty, they did discover many related properties of the developing embryo.

The source-sink model, first proposed by biologist Francis Crick in 1970, is a theoretical system for how morphogens distribute themselves across small fields of early embryonic cells. A morphogen is a substance that determines the fate and phenotype of a group of cells through a concentration gradient of itself across that group. Crick’s theory has been experimentally confirmed with several morphogens, most notably with the protein bicoid , the first discovered morphogen. The model provides a theoretical structure for the understanding of some features of early embryonic development.