Very few risk factors for choanal atresia have been identified. While causes are unknown, both genetic and environmental triggers are suspected. One study suggests that chemicals that act as endocrine disrupters may put an unborn infant at risk. A 2012 epidemiological study looked at atrazine, a commonly used herbicide in the U.S., and found that women who lived in counties in Texas with the highest levels of this chemical being used to treat agricultural crops were 80 times more likely to give birth to infants with choanal atresia or stenosis compared to women who lived in the counties with the lowest levels. Another epidemiological report in 2010 found even higher associations between increased incidents of choanal atresia and exposure to second-hand-smoke, coffee consumption, high maternal zinc and B-12 intake and exposure to anti-infective urinary tract medications.

The gene for Darwin's tubercle was once thought to be inherited in an autosomal dominant pattern with incomplete penetrance, meaning that those who possess the allele (version of a gene) will not necessarily present with the phenotype. However, genetic and family studies have demonstrated that the presence of Darwin's Tubercle may be more likely to be influenced by one's environment or developmental accidents than it is by genetics alone. There is no clear argument for whether the trait has significance in sexual dimorphism studies or age related studies. In some studies, there is clear data that Darwin's tubercle is not associated with sex. In contrast, others indicate that there is a correlation with sexual dimorphism between men and women, where men tend to have the tubercle more than women in some populations. Two studies indicate that older men tend to have greater expression of Darwin's tubercle than do older women.

Other causes may include:

- Diabetes mellitus

- Facial nerve paralysis, sometimes bilateral, is a common manifestation of sarcoidosis of the nervous system, neurosarcoidosis.

- Bilateral facial nerve paralysis may occur in Guillain–Barré syndrome, an autoimmune condition of the peripheral nervous system.

- Moebius syndrome is a bilateral facial paralysis resulting from the underdevelopment of the VII cranial nerve (facial nerve), which is present at birth. The VI cranial nerve, which controls lateral eye movement, is also affected, so people with Moebius syndrome cannot form facial expression or move their eyes from side to side. Moebius syndrome is extremely rare, and its cause or causes are not known.

Parents of a proband

- The parents of an affected individual are obligate heterozygotes and therefore carry one mutant allele.

- Heterozygotes (carriers) are asymptomatic.

Sibs of a proband

- At conception, each sibling of an affected individual has a 25% chance of being affected, a 50% chance of being an asymptomatic carrier, and a 25% chance of being unaffected and not a carrier.

- Once an at-risk sibling is known to be unaffected, the risk of his/her being a carrier is 2/3.

- Heterozygotes (carriers) are asymptomatic.

Offspring of a proband

- Offspring of a proband are obligate heterozygotes and will therefore carry one mutant allele.

- In populations with a high rate of consanguinity, the offspring of a person with GPR56-related BFPP and a reproductive partner who is a carrier of GPR56-related BFPP have a 50% chance of inheriting two GPR56 disease-causing alleles and having BFPP and a 50% chance of being carriers.

Other family members of a proband.

- Each sibling of the proband's parents is at a 50% risk of being a carrier

Most patients are diagnosed by the age of 10 years and Duane's is more common in girls (60 percent of the cases) than boys (40 percent of the cases). A French study reports that this syndrome accounts for 1.9% of the population of strabismic patients, 53.5% of patients are female, is unilateral in 78% of cases, and the left eye (71.9%) is affected more frequently than the right. Around 10–20% of cases are familial; these are more likely to be bilateral than non-familial Duane syndrome. Duane syndrome has no particular race predilection.

The cause of this condition is not known. A genetic basis is suspected. More than one case have been reported in three families.

There is no known cure for this syndrome. Patients usually need ophthalmic surgery and may also need dental surgery

Genetic counseling and screening of the mother's relatives is recommended.

Central facial palsy can be caused by a lacunar infarct affecting fibers in the internal capsule going to the nucleus. The facial nucleus itself can be affected by infarcts of the pontine arteries.

Hemifacial hypertrophy (also termed facial hemihypertrophy, facial hemihyperplasia, or Friedreich's disease) abbreviated as (HFH) is rare congenital disease characterized by unilateral enlargement of the head and teeth. It is classified as true HFH (THFH) with unilateral enlargement of the viscerocranium, and partial HFH (PHFH) in which not all structures are enlarged. Hemifacial hypertrophy can cause a wide spectrum of defects or may involve only muscle or bone. it is usually treated surgically. It is believed to be a minor form of hemihypertrophy.

This syndrome is due to mutations in the Nance Horan gene (NHS) which is located on the short arm of the X chromosome (Xp22.13).

The feature is present in approximately 10.4% of the Spanish adult population, 40% of Indian adults, and 58% of Swedish school children. This acuminate nodule represents the point of the mammalian ear. The trait can potentially be bilateral, meaning present on both ears, or unilateral, where it is only present on one ear. There is mixed evidence in regard to whether the bilateral or unilateral expression is related to population, or other factors. Some populations express full bilaterality, while others may express either unilateral or bilaterality. However, bilaterality appears to be more common than unilateral as it pertains to the expression of the trait.

In a newborn boy thought to have Fryns syndrome, Clark and Fenner-Gonzales (1989) found mosaicism for a tandem duplication of 1q24-q31.2. They suggested that the gene for this disorder is located in that region. However, de Jong et al. (1989), Krassikoff and Sekhon (1990), and Dean et al. (1991) found possible Fryns syndrome associated with anomalies of chromosome 15, chromosome 6, chromosome 8(human)and chromosome 22, respectively. Thus, these cases may all represent mimics of the mendelian syndrome and have no significance as to the location of the gene for the recessive disorder.

By array CGH, Slavotinek et al. (2005) screened patients with DIH and additional phenotypic anomalies consistent with Fryns syndrome for cryptic chromosomal aberrations. They identified submicroscopic chromosome deletions in 3 probands who had previously been diagnosed with Fryns syndrome and had normal karyotyping with G-banded chromosome analysis. Two female infants were found to have microdeletions involving 15q26.2 (see 142340), and 1 male infant had a deletion in band 8p23.1 (see 222400).

Facial femoral syndrome is a rare congenital disorder. It is also known as femoral dysgenesis, bilateral femoral dysgenesis, bilateral-Robin anomaly and femoral hypoplasia-unusual facies syndrome. The main features of this disorder are underdeveloped thigh bones (femurs) and unusual facial features.

The cause of fibular hemimelia is unclear. Purportedly, there have been some incidents of genetic distribution in a family; however, this does not account for all cases. Maternal viral infections, embryonic trauma, teratogenic environmental exposures or vascular dysgenesis (failure of the embryo to form a satisfactory blood supply) between four and seven weeks gestation are considered possible causes.

In an experimental mouse model, change in the expression of a homeobox gene led to similar, but bilateral, fibular defects.

The gene sal-like 4 (SALL4) or CHN1 ("chimerin") has became a mutated gene (protein) and it is also one of the cause of the body's Duane Syndrome.

Focal facial dermal dysplasia (FFDD) is a rare genetically heterogeneous group of disorders that are characterized by congenital bilateral scar like facial lesions, with or without associated facial anomalies. It is characterized by hairless lesions with fingerprint like puckering of the skin, especially at the temples, due to alternating bands of dermal and epidermal atrophy.

This condition is also known as Brauer syndrome (hereditary symmetrical aplastic nevi of temples, bitemporal aplasia cutis congenita, bitemporal aplasia cutis congenita: OMIM ) and Setleis syndrome (facial ectodermal dysplasia: OMIM ).

Asymmetric crying facies (ACF), also called Cayler cardiofacial syndrome, partial unilateral facial paresis and hypoplasia of depressor angula oris muscle, is a minor congenital anomaly caused by agenesis or hypoplasia of the depressor anguli oris muscle, one of the muscles that control the movements of the lower lip. This unilateral facial weakness is first noticed when the infant cries or smiles, affecting only one corner of the mouth and occurs on the left side in nearly 80% of cases. It is associated with other birth defects in more than 50% of cases.

When the hypoplasia of the depressor anguli oris muscle is associated with congenital cardiac defects, the term 'Cayler cardiofacial syndrome' is used.

Cayler syndrome is part of 22q11.2 deletion syndrome.

It was characterized by Cayler in 1969.

The syndrome was first described in 1943 and believed to be associated with racemose hemangiomatosis of the retina and arteriovenous malformations of the brain. It is non-hereditary and belongs to phakomatoses that do not have a cutaneous (pertaining to the skin) involvement. This syndrome can affect the retina, brain, skin, bones, kidney, muscles, and the gastrointestinal tract.

The number of new cases of Bell's palsy is about 20 per 100,000 population per year. The rate increases with age. Bell’s palsy affects about 40,000 people in the United States every year. It affects approximately 1 person in 65 during a lifetime.

A range of annual incidence rates have been reported in the literature: 15, 24, and 25–53 (all rates per 100,000 population per year). Bell’s palsy is not a reportable disease, and there are no established registries for people with this diagnosis, which complicates precise estimation.

In France, Aymé, "et al." (1989) estimated the prevalence of Fryns syndrome to be 0.7 per 10,000 births based on the diagnosis of 6 cases in a series of 112,276 consecutive births (live births and perinatal deaths).

In the movie City of Angels, Dr. Maggie Rice (played by Meg Ryan) correctly diagnoses the cause of a newborn baby's failure to thrive as due to choanal atresia.

Because the nerve emerges near the bottom of the brain, it is often the first nerve compressed when there is any rise in intracranial pressure. Different presentations of the condition, or associations with other conditions, can help to localize the site of the lesion along the VIth cranial nerve pathway.

The most common causes of VIth nerve palsy in adults are:

- More common: Vasculopathic (diabetes, hypertension, atherosclerosis), trauma, idiopathic.

- Less common: Increased intracranial pressure, giant cell arteritis, cavernous sinus mass (e.g. meningioma, Brain stem Glioblastoma aneurysm, metastasis), multiple sclerosis, sarcoidosis/vasculitis, postmyelography, lumbar puncture, stroke (usually not isolated), Chiari Malformation, hydrocephalus, intracranial hypertension, tuberculosis meningitis.

In children, Harley reports typical causes as traumatic, neoplastic (most commonly brainstem glioma), as well as idiopathic. Sixth nerve palsy causes the eyes to deviate inward (see: Pathophysiology of strabismus). Vallee et al. report that benign and rapidly recovering isolated VIth nerve palsy can occur in childhood, sometimes precipitated by ear, nose and throat infections.

Parinaud's Syndrome results from injury, either direct or compressive, to the dorsal midbrain. Specifically, compression or ischemic damage of the mesencephalic tectum, including the superior colliculus adjacent oculomotor (origin of cranial nerve III) and Edinger-Westphal nuclei, causing dysfunction to the motor function of the eye.

Classically, it has been associated with three major groups:

1. Young patients with brain tumors in the pineal gland or midbrain: pinealoma (intracranial germinomas) are the most common lesion producing this syndrome.

2. Women in their 20s-30s with multiple sclerosis

3. Older patients following stroke of the upper brainstem

However, any other compression, ischemia or damage to this region can produce these phenomena: obstructive hydrocephalus, midbrain hemorrhage, cerebral arteriovenous malformation, trauma and brainstem toxoplasmosis infection. Neoplasms and giant aneurysms of the posterior fossa have also been associated with the midbrain syndrome.

Vertical supranuclear ophthalmoplegia has also been associated with metabolic disorders, such as Niemann-Pick disease, Wilson's disease, kernicterus, and barbiturate overdose.

Type II appears to be due to mutations in the transcription factor TWIST2 on chromosome 2.

Type IV is due to mutations in the Cyp26c1 gene.

Bonnet–Dechaume–Blanc syndrome results mainly from arteriovenous malformations. These malformations are addressed previously in the article, under “Signs and Symptoms.” Due to lack of research, it is difficult to provide a specific mechanism for this disorder. However, a number of examinations, mentioned under “Diagnosis,” can be performed on subjects to investigate the disorder and severity of the AVMs.