There is no known cure for microcephaly. Treatment is symptomatic and supportive.

Numerous possible risk factors have been identified, including gestational diabetes, transplacental infections (the "TORCH complex"), first trimester bleeding, and a history of miscarriage. As well, the disorder is found twice as often in female babies. However, there appears to be no correlation between HPE and maternal age.

There is evidence of a correlation between HPE and the use of various drugs classified as being potentially unsafe for pregnant and lactating mothers. These include insulin, birth control pills, aspirin, lithium, thorazine, retinoic acid, and anticonvulsants. There is also a correlation between alcohol consumption and HPE, along with nicotine, the toxins in cigarettes and toxins in cigarette smoke when used during pregnancy.

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Affected individuals have a somewhat shortened lifespan. The maximum described lifespan is 67 years. Adults with 13q deletion syndrome often need support services to maintain their activities of daily living, including adult day care services or housing services.

Currently, research is focusing on identifying the role of the genes on 18p in causing the signs and symptoms associated with deletions of 18p. This will ultimately enable predictive genotyping.

TGIF-Mutations and deletions of this gene have been associated with holoprosencephaly. Penetrance is incomplete, meaning that a deletion of one copy of this gene is not in and of itself sufficient to cause holoprosencephaly. Ten to fifteen percent of people with 18p- have holoprosencephaly, suggesting that other genetic and environmental facts play a role in the etiology of holoprosencephaly in these individuals.

Medical management of children with Trisomy 13 is planned on a case-by-case basis and depends on the individual circumstances of the patient. Treatment of Patau syndrome focuses on the particular physical problems with which each child is born. Many infants have difficulty surviving the first few days or weeks due to severe neurological problems or complex heart defects. Surgery may be necessary to repair heart defects or cleft lip and cleft palate. Physical, occupational, and speech therapy will help individuals with Patau syndrome reach their full developmental potential. Surviving children are described as happy and parents report that they enrich their lives. The cited study grouped Edwards syndrome, which is sometimes survivable beyond toddlerhood, along with Patau, hence the median age of 4 at the time of data collection.

Although there is no cure for 13q deletion syndrome, symptoms can be managed, usually with the involvement of a neurologist, rehabilitation physician, occupational therapist, physiotherapist, psychotherapist, nutritionist, special education professional, and/or speech therapist. If the affected child's growth is particularly slow, growth hormone treatment can be used to augment growth. Plastic surgeries can repair cleft palates, and surgical repair or monitoring by a pediatric cardiologist can manage cardiac defects. Some skeletal, neurological, genitourinary, gastrointestinal, and ophthalmic abnormalities can be definitively treated with surgery. Endocrine abnormalities can often be managed medically. Special educators, speech and occupational therapists, and physiotherapists can help a child develop skills in and out of school.

Ethmocephaly is a type of cephalic disorder caused by holoprosencephaly. Ethmocephaly is the least common facial anomaly. It consists of a proboscis separating narrow-set eyes with an absent nose and microphthalmia (abnormal smallness of one or both eyes). Cebocephaly, another facial anomaly, is characterized by a small, flattened nose with a single nostril situated below incomplete or underdeveloped closely set eyes.

The least severe in the spectrum of facial anomalies is the median cleft lip, also called premaxillary agenesis.

Although the causes of most cases of holoprosencephaly remain unknown, some may be due to dominant or chromosome causes. Such chromosomal anomalies as trisomy 13 and trisomy 18 have been found in association with holoprosencephaly, or other neural tube defects. Genetic counseling and genetic testing, such as amniocentesis, is usually offered during a pregnancy if holoprosencephaly is detected. The recurrence risk depends on the underlying cause. If no cause is identified and the fetal chromosomes are normal, the chance to have another pregnancy affected with holoprosencephaly is about 6%.

There is no treatment for holoprosencephaly and the prognosis for individuals with the disorder is poor. Most of those who survive show no significant developmental gains. For children who survive, treatment is symptomatic. It is possible that improved management of diabetic pregnancies may help prevent holoprosencephaly, however there is no means of primary prevention.

More than 80% of children with Patau syndrome die within the first year of life. Children with the mosaic variation are usually affected to a lesser extent. In a retrospective Canadian study of 174 children with trisomy 13, median survival time was 12.5 days. One and ten year survival was 19.8% and 12.9% respectively.

Most fetuses with triploidy do not survive to birth, and those that do usually pass within days. As there is no treatment for Triploidy, palliative care is given if a baby survives to birth. If Triploidy is diagnosed during the pregnancy, termination is often offered as an option due to the additional health risks for the mother (preeclampsia, a life-threatening condition, or choriocarcinoma, a type of cancer). Should a mother decide to carry until term or until a spontaneous miscarriage occurs, doctors will monitor her closely in case either condition develops.

Mosaic triploidy has an improved prognosis, but affected individuals have moderate to severe cognitive disabilities.

At present, treatment for ring 18 is symptomatic, meaning that the focus is on treating the signs and symptoms of the conditions as they arise. To ensure early diagnosis and treatment, it is suggested that people with ring 18 undergo routine screenings for thyroid, hearing, and vision problems.

Animal studies have shown that administration of the drugs vinblastine, streptonigrin, triparano, sulfonamide, tetracycline, antihistamines, and antitumor agents to pregnant mothers have resulted in offspring born with iniencephaly. The drug clomiphene, a drug commonly used for ovulation stimulation in fertility treatments, has also been seen to be associated with iniencephaly.

In utero exposure to cocaine and other street drugs can lead to septo-optic dysplasia.

Pregnant mothers are advised to take folic acid supplements to reduce risk of iniencephaly by up to 70%. Pregnant mothers are also advised not to take antiepileptic drugs, diuretics, antihistamines, and sulfa drugs, all of which have been associated with increased risk for neural tube defects.

HPE is not a condition in which the brain deteriorates over time. Although serious seizure disorders, autonomic dysfunction, complicated endocrine disorders and other life-threatening conditions may sometimes be associated with HPE, the mere presence of HPE does not mean that these serious problems will occur or develop over time without any previous indication or warning. These abnormalities are usually recognized shortly after birth or early in life and only occur if areas of the brain controlling those functions are fused, malformed or absent.

Prognosis is dependent upon the degree of fusion and malformation of the brain, as well as other health complications that may be present.

The more severe forms of encephalopathy are usually fatal. This disorder consists of a spectrum of defects, malformations and associated abnormalities. Disability is based upon the degree in which the brain is affected. Moderate to severe defects may cause mental retardation, spastic quadriparesis, athetoid movements, endocrine disorders, epilepsy and other serious conditions; mild brain defects may only cause learning or behavior problems with few motor impairments.

Seizures may develop over time with the highest risk before 2 years of age and the onset of puberty. Most are managed with one medication or a combination of medications. Typically, seizures that are difficult to control appear soon after birth, requiring more aggressive medication combinations/doses.

Most children with HPE are at risk of having elevated blood sodium levels during moderate-severe illnesses, that alter fluid intake/output, even if they have no previous diagnosis of diabetes insipidus or hypernatremia.

A publication in the "Journal of Medical Genetics" in 1987 by Dr. I. Young and D. Madders of Leicester Royal Infirmary in the United Kingdom described the then-unknown condition when presenting "a stillborn male infant with pre-maxillary agenesis, bilateral microphthalmos, alobar holoprosencephaly, hydrocephalus, ventricular and atrial septal defects, small penis, bilateral cryptorchidism, and bilateral upper limb postaxial polydactyly." Both doctors noted no use of drugs, alcohol or cigarettes by the mother, and the baby was delivered normally after forty-one weeks of gestation. It was the first child of the parents, who were not related and went on to have another child successfully however this child was a stillbirth. There was severe overlapping of the bones of the skull and a cleft lip in addition to the bilateral polydactyly. Of the organs, Young and Madders noted missing parts of the tricuspid valve and other small cardiac defects, as well as the holoprosencephaly. Both doctors consulted various medical databases and, after discounting Meckel syndrome due to a lack of renal abnormalities, concluded that this was a hitherto unclassified condition. After later classification, it was later named for the two doctors, though at the time of publication it was termed 'pseudotrisomy 13' due to similarities with the condition Trisomy 13. Another case in 1989 with similar symptoms was also published as an example of 'pseudotrisomy 13', and there was no evidence of an extra chromosome, further suggesting that Trisomy 13 was a separate condition.

Currently, research is focusing on identifying the role of the genes on 18p and 18q in causing the signs and symptoms associated with deletions of 18p and/or 18q. This will ultimately enable predictive genotyping.Thus far, several genes on chromosome 18 have been linked with a phenotypic effect.

TGIF - Mutations and deletions of this gene, which is located on18p, have been associated with holoprosencephaly. Penetrance is incomplete, meaning that a deletion of one copy of this gene is not in and of itself sufficient to cause holoprosencephaly. Ten to fifteen percent of people with 18p- have holoprosencephaly, suggesting that other genetic and environmental facts play a role in the etiology of holoprosencephaly in these individuals.

TCF4 – In 2007, deletions of or point mutations in this gene, which is located on 18q, were identified as the cause of Pitt-Hopkins disease. This is the first gene that has been definitively shown to directly cause a clinical phenotype when deleted. If a deletion includes the TCF4 gene (located at 52,889,562-52,946,887), features of Pitt-Hopkins may be present, including abnormal corpus callosum; short neck; small penis; accessory and wide-spaced nipples; broad or clubbed fingers; and sacral dimple. Those with deletions inclusive of TCF4 have a significantly more severe cognitive phenotype.

TSHZ1 - Point mutations and deletions of this gene, located on 18q, are linked with congenital aural atresia Individuals with deletions inclusive of this gene have a 78% chance of having aural atresia.

"Critical regions" – Recent research has narrowed the critical regions for four features of the distal 18q- phenotype down to a small segment of distal 18q, although the precise genes responsible for those features remain to be identified.

"Haplolethal Regions" - There are two regions on chromosome 18 that has never been found to be deleted. They are located between the centromere and 22,826,284 bp (18q11.2) and between 43,832,732 and 45,297,446 bp (18q21.1). It is hypothesized that there are genes in these regions that are lethal when deleted.

Prognosis is poor. Previous research suggested a 100% mortality rate for those with acrania. This disease is rare, occurring in 1 in 20,000 live births.

In order to better manage an acrania diagnosis, early detection is of extreme importance so that actions may be taken to help the mother and child. Families may choose either to terminate the pregnancy, or to carry the child to term. Acrania may cause a fetus to spontaneously abort before reaching term.

Microcephaly generally is due to the diminished size of the largest part of the human brain, the cerebral cortex, and the condition can arise during embryonic and fetal development due to insufficient neural stem cell proliferation, impaired or premature neurogenesis, the death of neural stem cells or neurons, or a combination of these factors. Research in animal models such as rodents has found many genes that are required for normal brain growth. For example, the Notch pathway genes regulate the balance between stem cell proliferation and neurogenesis in the stem cell layer known as the ventricular zone, and experimental mutations of many genes can cause microcephaly in mice, similar to human microcephaly. In addition, viruses such as cytomegalovirus (CMV) or Zika have been shown to infect and kill the primary stem cell of the brain—the radial glial cell, resulting in the loss of future daughter neurons. The severity of the condition may depend on the timing of infection during pregnancy.

Triploid syndrome, also called triploidy, is an extremely rare chromosomal disorder, in which a fetus has three copies of every chromosome instead of the normal two. If this occurs in only some cells, it is called mosaic triploidy, and is less severe.

Valproate toxicity "in utero" has been implicated as a possible etiology of septo-optic dysplasia.

Cerebellar agenesis is a rare condition in which a brain develops without the cerebellum. The cerebellum controls smooth movement, and when it does not develop, the rest of the brain must compensate, which it cannot do completely. The condition is not fatal on its own, but people born without a cerebellum experience severe developmental delays, language deficits, and neurological abnormalities. As children with cerebellar agenesis get older, their movements usually improve. It can co-exist with other severe malformations of the central nervous system, like anencephaly, holoprosencephaly, and microencephaly.

The condition was first reported in 1831. 10 cases had been reported as of 1998. Agenesis of one half or another part of the cerebellum is more common than complete agenesis.

Cerebellar agenesis can be caused by mutations in the PTF1A gene.

Young–Madders syndrome, alternatively known as Pseudotrisomy 13 syndrome or holoprosencephaly–polydactyly syndrome, is a genetic disorder resulting from defective and duplicated chromosomes which result in holoprosencephaly, polydactyly, facial malformations and mental retardation, with a significant variance in the severity of symptoms being seen across known cases. Many cases often suffer with several other genetic disorders, and some have presented with hypoplasia, cleft lip, cardiac lesions and other heart defects. In one case in 1991 and another in 2000 the condition was found in siblings who were the product of incest. Many cases are diagnosed prenatally and often in siblings. Cases are almost fatal in the prenatal stage with babies being stillborn.

Though it is now thought that earlier cases were misdiagnosed as other genetic disorders with similar pathology—such as Smith–Lemli–Opitz syndrome—the earliest publicised recognition of the condition as a new, hitherto unclassified, genetic disorder was made by two British doctors in Leicester in 1987. Though they identified the condition, later named for them, they did not identify the genetic anomalies responsible but suspected a link with trisomy 13 due to the similar symptoms. With only one or two occurrences documented towards the end of the decade, a group of eight doctors published a five-patient case-study in 1991 which identified the likely chromosomal factors that caused the condition, similar to but distinct from trisomy 13, and gave it the name 'holoprosencephaly–polydactyly syndrome' based on its two most prolific presenting conditions. Later research showed that the condition could manifest in patients with normal karyotypes, without duplication of the chromosomes, and the most recent genetic research implicates problems with the gene code FBXW11 as a likely cause.

There is no standard treatment for hydranencephaly. Treatment is symptomatic and supportive. Hydrocephalus may be treated with surgical treatment of a shunt, which often grants a much better prognosis and greater quality of life.

The prognosis for children with hydranencephaly is generally quite poor. Death often occurs in the first year of life, but other children may live several years.

Medical text identifies that hydranencephalic children simply have only their brain stem function remaining, thus leaving formal treatment options as symptomatic and supportive. Severe hydrocephalus causing macrocephaly, a larger than average head circumference, can easily be managed by placement of a shunt and often displays a misdiagnosis of another lesser variation of cephalic condition due to the blanketing nature of hydrocephalus. Plagiocephaly, the asymmetrical distortion of the skull, is another typical associated condition that is easily managed through positioning and strengthening exercises to prevent torticollis, a constant spasm or extreme tightening of the neck muscles.

In 1963, a doctor studied two female infants who showed symptoms of mental retardation, congenital cataracts, epileptic fits and small stature. The two girls died at the age of 4 and 8 months. The autopsy revealed renal tubular necrosis and encephalopathy.