There is no cure for holoprosencephaly. Severe forms are fatal. For children with milder forms, treatment is directed at the symptoms rather than the disease.

The prognosis for an infant born with holoprosencephaly depends on the severity of the cerebral and other defects. The prognosis for an infant with severe holoprosencephaly is poor; most do not survive past six months, and those that do are likely to suffer profound mental-retardation. At the mild end of the spectrum, where brain development may be nearly normal, a normal life-spanis likely.

Ultrasonic examination of the fetal brain has made early detection of holoprosencephaly common. In infants born live, a preliminary diagnosis may be based on extremely small head size (microcephaly ) and on examination of the face.

The life span of individuals with holoprosencephaly can vary based on the severity of their condition and associated health complications. Some individuals with milder forms of holoprosencephaly may live into adulthood with appropriate medical care, while those with more severe forms may have a shorter life expectancy, often dying in infancy or childhood. It is important for individuals with holoprosencephaly to receive interdisciplinary care to manage their medical needs and support their quality of life.

Holoprosencephaly has no single cause, but about half of all cases are associated with abnormal karyotype (abnormal numbers of chromosomes), especially trisomy 13 (extra copy of chromosome 13) and trisomy 15 (extra copy of chromosome 15).