It is important to understand where hESCs come from in order to understand the ethical arguments that surround them, as well as their enormous, innate biological potential. After the human egg is fertilized by the sperm, the resultant single cell (called a zygote) starts dividing and multiplying. To get hESCs, cells are isolated from early-stage embryos, four or five days post-fertilization (they have not yet implanted in the uterus). At this point, the fertilized egg has developed into a hollow, fluid-filled sphere made up of approximately 150 cells. This stage is called a blastocyst.

The blastocyst contains three distinct areas: the trophoblast, which is the surrounding outer layer of cells that later becomes the placenta; the blastocoel, which is a fluid-filled cavity within the blastocyst; and the inner cell mass, which is a cluster of cells inside the blastocyst that can become a fetus. Embryonic stem cells can be created from cells taken from the inner cell mass. Because these cells are taken from such an early stage in development, they have the ability to become cells of any tissue type, which is called being "pluripotent."

The pluripotency of hESCs is probably the trait that contributes most to their enormous potential, both as cellular models of human development and disease, as well as for uses in regenerative medicine. This trait is what mainly separates hESCs from adult stem cells, which are called multipotent or unipotent, meaning they are only able to become a more select group of cell types. Adult stem cells are also more limited in their cellular lifespan compared to hESCs.