It is most often caused by genetic abnormalities that interfere with the growth of the cerebral cortex during the early months of fetal development. It is associated with Down's syndrome, chromosomal syndromes, and neurometabolic syndromes. Babies may also be born with microcephaly if, during pregnancy, their mother abused drugs or alcohol, became infected with a cytomegalovirus, rubella (German measles), or varicella (chickenpox) virus, was exposed to certain toxic chemicals or had untreated phenylketonuria (PKU).

There is no treatment for microcephaly that can return a child's head to a normal size or shape. Treatment focuses on ways to decrease the impact of the associated deformities and neurological disabilities. Children with microcephaly and developmental delays are usually evaluated by a pediatric neurologist and followed by a medical management team. Early childhood intervention programs that involve physical, speech, and occupational therapists help to maximize abilities and minimize dysfunction. Medications are often used to control seizures, hyperactivity, and neuromuscular symptoms. Genetic counseling may help families understand the risk of microcephaly in subsequent pregnancies.