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Development and differentiation includes processes by which a multicellular organism starts out from a single cell, a zygote, and gives rise to multiple cell types, forming different tissues and organs. Development comprises cell division, tissue and organ formation, body axis determination and cellular differentiation.

During development, cells must divide to form tissues and organs, while also they must differentiate into many diverse cell types with their distinctive features and functions. The totipotent zygote can give rise to all the cell types in the body and the placenta. As development progresses, cells potential to make up all cell types diminishes, and the embryonic stem cells become pluripotent, being able to give rise to all the cells of the body, except the placenta. The cells later differentiate into 3 germ layers: ectoderm, mesoderm and endoderm, and they conserve the ability to give rise to the cell types in their own lineage and not others. This is mostly under genetic control and different cell types start expressing different gene sets.

Differentiation is the process in which a cell develops its final cell type identity, and specific gene expression patterns allow the cell to synthesize RNA and protein specific for their structure and function. Not all cells in the body differentiate, some cells retain their ability to divide and produce multiple cell types. These include adult stem cells and cord blood stem cells, which are multipotent, as they have the ability to produce more than one cell type, but not all cell types. Hematopoietic stem cells are adult stem cells which give rise to the different cell types in blood. Stem cells undergo asymmetric cell division, producing two different daughter cells, one preserves the ability to self-renew and continues to be a stem cell, while the other becomes a differentiated cell.

An important group of genes controlling cellular differentiation during development are the HOX genes. They are not expressed in embryonic stem cells, but are expressed later by tissue stem cells in order to differentiate into their lineages and they are involved in determination of anterior-posterior body axis. Embryonic stem cells express transcription factors important for pluripotency, such as NANOG and OCT3/4 (POU5F1). Somatic cells can be reprogrammed to become induced pluripotent cells (iPS) by introducing transcription factors SOX2, KLF4, NANOG and OCT3/4.

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