The clinical presentation of HFM is quite variable. The severity may depend on the extent of the area with an insufficient blood supply "in utero", and the gestational age of the fetus at which this occurs. In some people, the only physical manifestation may be a small and underdeveloped external ear. In more severe cases, multiple parts of the face may be affected. Some people with HFM may have sensorineural hearing loss and decreased visual acuity or even blindness.

Goldenhar syndrome can be thought of as a particularly severe form of HFM, in which extracranial anomalies are present to some extent. Some of the internal organs (especially the heart, kidneys, and lungs) may be underdeveloped, or in some cases even absent altogether. The affected organs are typically on the same side as the affected facial features, but bilateral involvement occurs in approximately 10% of cases. Deformities of the vertebral column such as scoliosis may also be observed in Goldenhar syndrome.

While there is no universally accepted grading scale, the OMENS scale (standing for Orbital, Mandible, Ear, Nerves and Soft tissue) was developed to help describe the heterogeneous phenotype that makes up this sequence or syndrome.

Intellectual disability is not typically seen in people with HFM.

The condition is also known by various other names:

- Lateral facial dysplasia

- First and second branchial arch syndrome

- Oral-mandibular-auricular syndrome

- Otomandibular dysostosis

- Craniofacial microsomia

Chief markers of Goldenhar syndrome are incomplete development of the ear, nose, soft palate, lip, and mandible on usually one side of the body. Additionally, some patients will have growing issues with internal organs, especially heart, kidneys, and lungs. Typically, the organ will either not be present on one side or will be underdeveloped. Note that while it is more usual for there to be problems on only one side, it has been known for defects to occur bilaterally (approximate incidence 10% of confirmed GS cases).

Other problems can include severe scoliosis (twisting of the vertebrae), limbal dermoids, and hearing loss (see hearing loss with craniofacial syndromes), and deafness or blindness in one or both ears/eyes, Granulosa cell tumors may be associated as well.

Two key features of AOS are aplasia cutis congenita with or without underlying bony defects and terminal transverse limb defects. Cutis aplasia congenita is defined as missing skin over any area of the body at birth; in AOS skin aplasia occurs at the vertex of the skull. The size of the lesion is variable and may range from solitary round hairless patches to complete exposure of the cranial contents. There are also varying degrees of terminal limb defects (for example, shortened digits) of the upper extremities, lower extremities, or both. Individuals with AOS may have mild growth deficiency, with height in the low-normal percentiles. The skin is frequently observed to have a mottled appearance (cutis marmorata telangiectatica congenita). Other congenital anomalies, including cardiovascular malformations, cleft lip and/or palate, abnormal renal system, and neurologic disorders manifesting as seizure disorders and developmental delay are sometimes observed. Variable defects in blood vessels have been described, including hypoplastic aortic arch, middle cerebral artery, pulmonary arteries. Other vascular abnormalities described in AOS include absent portal vein, portal sclerosis, arteriovenous malformations, abnormal umbilical veins, and dilated renal veins.

Common relevant features of acrocephalosyndactyly are a high-arched palate, pseudomandibular prognathism (appearing as mandibular prognathism), a narrow palate, and crowding of the teeth.

As a result of the changes to the developing embryo, the symptoms are very pronounced features, especially in the face. Low-set ears are a typical characteristic, as in all of the disorders which are called branchial arch syndromes. The reason for this abnormality is that ears on a foetus are much lower than those on an adult. During normal development, the ears "travel" upward on the head; however, in Crouzon patients, this pattern of development is disrupted. Ear canal malformations are extremely common, generally resulting in some hearing loss. In particularly severe cases, Ménière's disease may occur.

The most notable characteristic of Crouzon syndrome is craniosynostosis, as described above; however it usually presents as brachycephaly resulting in the appearance of a short and broad head. Exophthalmos (bulging eyes due to shallow eye sockets after early fusion of surrounding bones), hypertelorism (greater than normal distance between the eyes), and psittichorhina (beak-like nose) are also symptoms. Additionally, external strabismus is a common occurrence, which can be thought of as opposite from the eye position found in Down syndrome. Lastly, hypoplastic maxilla (insufficient growth of the midface) results in relative mandibular prognathism (chin appears to protrude despite normal growth of mandible) and gives the effect of the patient having a concave face. Crouzon syndrome is also associated with patent ductus arteriosus (PDA) and aortic coarctation.

For reasons that are not entirely clear, most Crouzon patients also have noticeably shorter humerus and femur bones relative to the rest of their bodies than members of the general population. A small percentage of Crouzon patients also have what is called "Type II" Crouzon syndrome, distinguished by partial syndactyly.

Goldenhar syndrome (also known as oculo-auriculo-vertebral (OAV) syndrome) is a rare congenital defect characterized by incomplete development of the ear, nose, soft palate, lip, and mandible. It is associated with anomalous development of the first branchial arch and second branchial arch. Common clinical manifestations include limbal dermoids, preauricular skin tags, and strabismus.

The term is sometimes used interchangeably with hemifacial microsomia, although this definition is usually reserved for cases without internal organ and vertebrae disruption.

It affects between 1/3,500 and 1/26,000 live births, with a male:female ratio of 3:2.

People with Möbius syndrome are born with facial paralysis and the inability to move their eyes laterally. Often, the upper lip is retracted due to muscle shrinkage. Occasionally, the cranial nerves V and VIII are affected. If cranial nerve VIII is affected, the person experiences hearing loss.

Other symptoms that sometimes occur with Möbius syndrome are:

- Limb abnormalities—clubbed feet, missing fingers or toes

- Chest-wall abnormalities (Poland Syndrome)

- Crossed eyes (strabismus)

- Difficulty in breathing and/or in swallowing

- Corneal erosion resulting from difficulty in blinking

Children with Möbius syndrome may have delayed speech because of paralysis of muscles that move the lips, soft palate, and tongue root. However, with speech therapy, most people with Möbius syndrome can develop understandable speech. Möbius syndrome has been associated with increased occurrence of the symptoms of autism. However, some children with Möbius syndrome are mistakenly labeled as intellectually disabled or autistic because of their expressionless faces, strabismus, and frequent drooling.

The cranial malformations are the most apparent effects of acrocephalosyndactyly. Craniosynostosis occurs, in which the cranial sutures close too soon, though the child's brain is still growing and expanding. Brachycephaly is the common pattern of growth, where the coronal sutures close prematurely, preventing the skull from expanding frontward or backward, and causing the brain to expand the skull to the sides and upwards. This results in another common characteristic, a high, prominent forehead with a flat back of the skull. Due to the premature closing of the coronal sutures, increased cranial pressure can develop, leading to mental deficiency. A flat or concave face may develop as a result of deficient growth in the mid-facial bones, leading to a conditir prognathism. Other features of acrocephalosyndactyly may include shallow bony orbits and broadly spaced eyes. Low-set ears are also a typical characteristic of branchial arch syndromes.

The general presentation is of a skin-covered nodule, papule, or nodule of the skin surface, usually immediately anterior to the auricle. However, it may be anywhere within the periauricular tissues. Bilateral presentation can be seen.

The several components or degrees of development range from an ear tag, preauricular appendage, preauricular tag, or accessory tragus, to supernumerary ears or polyotia. It is a relatively common congenital anomaly of the first branchial arch or second branchial arches. Other anomalies may be present concurrently, including cleft palate, cleft lip, or mandibular hypoplasia. There is a known association with Goldenhar syndrome (oculo-auriculo-vertebral syndrome) and with Wildervanck syndrome. There may also be an association with congenital cartilaginous rest of the neck.

Nasodigitoacoustic syndrome is congenital and is characterized by a number of nasal, facial and cranial features. These include a broad and high, sometimes depressed nasal bridge (top of the nose, between the eyes) and a flattened nasal tip. This can give the nose a shortened, arch-like appearance. Hypertelorism (unusually wide-set eyes), prominent frontal bones and supraorbital ridge (the eyebrow ridge), bilateral epicanthic folds (an extra flap of skin over the eyelids), a broad forehead and an overall enlarged head circumference have also been observed. A bulging of the upper lip with an exaggerated cupid's bow shape, and maxillary hypoplasia (underdevelopment of the upper jaw) with retraction have also been reported.

Several anomalies affecting the digits (fingers and toes) have been observed with the syndrome. A broadening of the thumbs and big toes (halluces) was reported in two brothers. The broadening was apparent in all distal phalanges of the fingers, although the pinkies were unaffected yet appeared to be clinodactylic (warped, or bent toward the other fingers). Additional eports described this broadness of the thumbs and big toes, with brachydactyly (shortness) in the distal phalanges of the other digits except the pinkies in affected individuals. On X-rays of a two-year-old boy with the disorder, the brachydactyly was shown to be caused by shortening of epiphyses (joint-ends) of the distal phalanges. The broadness and brachydactyly of the big toes in particular may give them a stunted, rounded and stub-like appearance.

The auditory, or "acoustic" abnormalities observed with the syndrome include sensorineural hearing loss and hoarseness. Two affected Turkish brothers with a mild form of this hearing loss, and a hoarse voice were reported. A laryngoscopic examination of both brothers revealed swelling of the vocal cords, and a malformed epiglottis. Sensorineural-associated hearing impairment and hoarsness was also observed in a 10-year-old girl and her father, and in a number of other cases.

Other characteristics seen with the syndrome include developmental delay, growth retardation, pulmonary stenosis (an obstruction of blood-flow from the right ventricle of the heart to the pulmonary artery) with associated dyspnea (shortness of breath), and renal agenesis (failure of the kidneys to develop during the fetal period). Undescended testes, hyperactivity and aggressive behavior have also been noted.

Crouzon syndrome is an autosomal dominant genetic disorder known as a branchial arch syndrome. Specifically, this syndrome affects the first branchial (or pharyngeal) arch, which is the precursor of the maxilla and mandible. Since the branchial arches are important developmental features in a growing embryo, disturbances in their development create lasting and widespread effects.

This syndrome is named after Octave Crouzon, a French physician who first described this disorder. He noted the affected patients were a mother and her daughter, implying a genetic basis. First called "craniofacial dysostosis", the disorder was characterized by a number of clinical features. This syndrome is caused by a mutation in the fibroblast growth factor receptor II, located on chromosome 10.

Breaking down the name, "craniofacial" refers to the skull and face, and "dysostosis" refers to malformation of bone.

Now known as Crouzon syndrome, the characteristics can be described by the rudimentary meanings of its former name. What occurs is that an infant's skull and facial bones, while in development, fuse early or are unable to expand. Thus, normal bone growth cannot occur. Fusion of different sutures leads to different patterns of growth of the skull.

Examples include: trigonocephaly (fusion of the metopic suture), brachycephaly (fusion of the coronal suture), dolichocephaly (fusion of the sagittal suture), plagiocephaly (unilateral premature closure of lambdoid and coronal sutures), oxycephaly (fusion of coronal and lambdoidal sutures), Kleeblattschaedel (premature closure of all sutures).

Adams–Oliver syndrome (AOS) is a rare congenital disorder characterized by defects of the scalp and cranium (cutis aplasia congenita), transverse defects of the limbs, and mottling of the skin.

Abnormal development of the skeletal portions of the second arch

1. Nondifferentiation of the stapes, with resultant absence of round and oval window.

2. Abnormal course of the facial nerve.

Skull base abnormalities

1. Hypoplasia of the petrous temporal bone.

2. Hypoplastic and sclerotic petrous apex may mimic labyrinthitis ossificans.

3. Platybasia.

4. Aberrant course of jugular veins.

The primary (baby) teeth generally start coming in by 6 months of age, and all 20 teeth may be in by two and a half years of age. The eruption timing varies greatly. There may be an incomplete formation of the enamel on the teeth (enamel hypoplasia) that makes the teeth more vulnerable to caries (cavities). There may be missing teeth eruptions. If the infant is not closing down properly, the lower jaws become more noticeably deficient (micrognathia or retrognathia). The front teeth may not touch when the child closes down because the back teeth have overerrupted or because of incomplete formation of the maxilla. This condition is called an anterior open bite and has facial/skeletal implications. The saliva may be thick, or the infant may have a dry mouth.

Michel aplasia, also known as complete labyrinthine aplasia (CLA), is a congenital abnormality of the inner ear. It is characterized by the bilateral absence of differentiated inner ear structures and results in complete deafness (anacusis).

Michel aplasia should not be confused with michel dysplasia. It may affect one or both ears.

"Aplasia" is the medical term for body parts that are absent or do not develop properly. In Michel aplasia, the undeveloped (anaplastic) body part is the bony labyrinth of the inner ear. Other nearby structures may be underdeveloped as well.

Nasodigitoacoustic syndrome, also called Keipert syndrome, is a rare congenital syndrome first described by J.A. Keipert and colleagues in 1973. The syndrome is characterized by a mishaped nose, broad thumbs and halluces (the big toes), brachydactyly, sensorineural hearing loss, facial features such as hypertelorism (unusually wide-set eyes), and developmental delay. It is believed to be inherited in an X-linked recessive manner, which means a genetic mutation causing the disorder is located on the X chromosome, and while two copies of the mutated gene must be inherited for a female to be born with the disorder, just one copy is sufficient to cause a male to be born with the disorder. Nasodigitoacoustic syndrome is likely caused by a mutated gene located on the X chromosome between positions Xq22.2–q28. The incidence of the syndrome has not been determined, but it is considered to affect less than 200,000 people in the United States, and no greater than 1 per 2,000 in Europe. It is similar to Keutel, Muenke, Rubinstein and Teunissen-Cremers syndrome.

“Branchio” refers to the branchial arches, also known as the pharyngeal arches, of the affected individual. The branchial arches are structures in the developing embryo that give rise to certain tissues in the neck and facial area. In individuals affected by this condition, the branchial arches fail to develop properly. This leads to some of the physical conditions of this syndrome, which include abnormal patches of skin on the neck and face region and can be abnormally hairy, thin or red and with a high number of blood vessels. “Oculo” refers to the eyes. Individuals have vision impairment due to several malformations in the eyes such as small eyeballs, blockage in the tear ducts or lacking eyes completely. “Facial” refers to the face; those affected can have several abnormalities in that region. These abnormalities include a cleft lip, a cleft palate which is an opening in the roof of the mouth, widely spaced eyes (hypertelorism), sharp corners of the mouth that point upward, a broad nose that can include a flattened tip, along with several deformations of both the external and middle ear structures. This syndrome is restricted to the face, but it can also cause underdeveloped or malformed kidneys.

First arch syndromes are congenital defects caused by a failure of neural crest cells to migrate into the first pharyngeal arch. They can produce facial anomalies. Examples of first arch syndromes include Treacher Collins syndrome and Pierre Robin syndrome.

Marfanoid (or Marfanoid habitus) is a constellation of symptoms resembling those of Marfan syndrome, including long limbs, with an arm span that exceeds the height of the individual, and a crowded oral maxilla, sometimes with a high arch in the palate, arachnodactyly, and hyperlaxity.

Associated conditions include:

- Multiple endocrine neoplasia type 2B

- Homocystinuria

- Ehlers-Danlos syndrome

- Possibly Asperger syndrome

Arachnodactyly ("spider fingers") or achromachia is a condition in which the fingers and toes are abnormally long and slender, in comparison to the palm of the hand and arch of the foot. Also, the individual's thumbs tend to also be pulled inwards towards the palm. It can be present at birth or develop in later life.

This feature can occur on its own, with no underlying health problems. However, it can also be associated with certain medical conditions. Examples include Marfan syndrome, Ehlers-Danlos syndrome, Loeys–Dietz syndrome, congenital contractural arachnodactyly, and homocystinuria.

Arachnodactyly has been linked to mutations in both fibrillin-1 and fibrillin-2 genes.

Lachiewicz–Sibley syndrome is a rare autosomal dominant disorder characterized by preauricular pits and renal disease. Persons with this disease may have hypoplasic kidneys or proteinuria. This disease was first described in a Caucasian family of British and Irish descent that emigrated to Ohio in the 19th century before settling in Nebraska. Many of the members of this family still live in Nebraska, although the relatives are now scattered throughout the country.

Unlike branchio-oto-renal (BOR) syndrome, Lachiewicz–Sibley syndrome is characterized by only preauricular pitting and renal disease. Persons with BOR syndrome also present with hearing loss, branchial fistulas or cysts, malformed ears, and lacrimal stenosis. Other anomalies in BOR syndrome may include a long narrow face, a deep overbite, and facial paralysis.

It was characterized in 1985.

Branchio-oculo-facial syndrome (BOFS) is a disease that arises from a mutation in the TFAP2A gene. It is a rare autosomal dominant disorder that starts to affect a child's development before birth. Symptoms of this condition include skin abnormalities on the neck, deformities of the ears and eyes, and other distinctive facial features such a cleft lip along with slow growth, mental retardation and premature graying of hair.