The disorder may stem from a wide variety of conditions that cause abnormal growth of the brain, or from syndromes associated with chromosomal abnormalities. Two copies of a loss-of-function mutation in one of the microcephalin genes causes primary microcephaly.

Microcephaly is a disorder characterized by a small brain and may be caused by a disturbance in the proliferation of nerve cells. Microcephaly may also be associated with maternal problems such as alcoholism (which can result in the Fetal alcohol syndrome disability), diabetes, or rubella (German measles). A genetic factor may play a role in causing some cases of microcephaly. Affected newborns generally have striking neurological defects and seizures. Severely impaired intellectual development is common, but disturbances in motor functions may not appear until later in life.