The human X chromosome contains over ten times the number of genes as in the Y chromosome. Since males have only one X chromosome, and females have two, one might expect females to produce twice as many of the proteins, with undesirable results.

Instead, in order to avoid this potential issue, female mammalian cells inactivate nearly all the genes in one of their X chromosomes during early embryonic development. In the nuclear envelope surrounding the cell nucleus, the inactivated X chromosome condenses into a small, dense ball called a Barr body. In this state, most of the X-linked genes are not accessible to transcription.

In placental mammals, the inactivated X chromosome—maternal or paternal⁠—is randomly determined (marsupials, however, preferentially inactivate the paternal X chromosome). X inactivation in one cell is also independent of X inactivation in other cells. Thus, about half the embryonic cells inactivate the maternal X copy; the remaining half inactivate the paternal copy, producing a mosaic. When these cells replicate, they produce cells with the same X chromosome inactivated. Notably, Barr bodies get reactivated in cells within the ovaries that become eggs.

X inactivation accounts for the appearance of female tortoiseshell and calico cats. These cats are heterozygous for a gene with alleles for black fur and orange fur located on the X chromosome. Their mottled coats result from random inactivation of the black and orange fur alleles in groups of cells (calico cats also have white fur patches that are caused by a different chromosome). While male tortoiseshell and calico cats exist, they have an extra X chromosome and are generally infertile.

X inactivation reduces the severity of conditions caused by extra X chromosomes. Males with Klinefelter syndrome form Barr bodies to inactivate their extra X chromosome. Females with Triple X syndrome form additional Barr bodies for their excess X chromosome or chromosomes.