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The brain develops in an intricately orchestrated sequence of stages. It changes in shape from a simple swelling at the front of the nerve cord in the earliest embryonic stages, to a complex array of areas and connections. Neurons are created in special zones that contain stem cells, and then migrate through the tissue to reach their ultimate locations. Once neurons have positioned themselves, their axons sprout and navigate through the brain, branching and extending as they go, until the tips reach their targets and form synaptic connections. In a number of parts of the nervous system, neurons and synapses are produced in excessive numbers during the early stages, and then the unneeded ones are pruned away.

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For vertebrates, the early stages of neural development are similar across all species. As the embryo transforms from a round blob of cells into a wormlike structure, a narrow strip of ectoderm running along the midline of the back is induced to become the neural plate, the precursor of the nervous system. The neural plate folds inward to form the neural groove, and then the lips that line the groove merge to enclose the neural tube, a hollow cord of cells with a fluid-filled ventricle at the center. At the front end, the ventricles and cord swell to form three vesicles that are the precursors of the prosencephalon (forebrain), mesencephalon (midbrain), and rhombencephalon (hindbrain).

At the next stage, the forebrain splits into two vesicles called the telencephalon (which will contain the cerebral cortex, basal ganglia, and related structures) and the diencephalon (which will contain the thalamus and hypothalamus). At about the same time, the hindbrain splits into the metencephalon (which will contain the cerebellum and pons) and the myelencephalon (which will contain the medulla oblongata). Each of these areas contains proliferative zones where neurons and glial cells are generated; the resulting cells then migrate, sometimes for long distances, to their final positions.

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