Pathophysiology of Rett syndrome is discussed in relation to the MeCP2 gene. The brainstem aminergic neurons are affected in early infancy, resulting in failure in locomotion, head growth and language. The severity of symptoms is related to the specific loci of a mutation on the methylbinding domain which shows correlation with the degree of heterochronation disturbance. The secondary involvement of dopamine neurons together with dysfunction of cholinergic neurons, causes stereotyped movements and regression. In the normal fetus brain MeCP2 is expressed diffusely, and subsequently disappears early in the cortex and later in the brainstem. Abnormalities in the MeCP2 gene may alter these processes and cause age-dependent symptoms.