Almost all cases of synkinesis develop as a sequel to nerve trauma (the exception is when it is congenitally acquired as in Duane-Retraction Syndrome and Marcus Gunn phenomenon). Trauma to the nerve can be induced in cases such as surgical procedures, nerve inflammation, neuroma

, and physical injury.

Synkinesis is the result from miswiring of nerves after trauma. This result is manifested through involuntary muscular movements accompanying voluntary movements. For example, voluntary smiling will induce an involuntary contraction of the eye muscles causing the eye to squint when smiling. Most commonly involved are facial muscles and the extraocular muscles, rarely the hands are performing mirror movements.

Causes are diverse and include nerve trauma with improper healing, or nerve degeneration, as in the course of Parkinson´s disease. In congenital cases, mutations of genes involved in nerve growth, specifically axonal growth have been found. Rarely, it is part of syndromes with neuroendocrine problems such as Kallman syndrome.

The prognosis is usually good with normal intelligence and lifespan. Treatment depends on the cause, but is largely conservative with facial retraining or mime therapy, if needed, while Botox and surgery are used as last resort.

Inverse Marcus Gunn phenomenon is a rare condition that causes the eyelid to fall upon opening of the mouth. In this case, trigeminal innervation to the pterygoid muscles of the jaw is associated with an inhibition of the branch of the oculomotor nerve to the levator palpebrae superioris, as opposed to stimulation in Marcus Gunn jaw-winking.

Marcus Gunn phenomenon, also known as Marcus Gunn jaw-winking or trigemino-oculomotor synkinesis, is an autosomal dominant condition with incomplete penetrance, in which nursing infants will have rhythmic upward jerking of their upper eyelid. This condition is characterized as a synkinesis: when two or more muscles that are independently innervated have either simultaneous or coordinated movements.

Common physiologic examples of synkineses occur during sucking, chewing, or conjugate eye movements. There are also several abnormal cranial nerve synkineses, both acquired and congenital. Marcus Gunn jaw-winking is an example of a pathologic congenital synkinesis.

First described by the ophthalmologist Marcus Gunn in 1883, this condition presents in approximately 5% of neonates with congenital ptosis. This condition has been associated with amblyopia (in 54% of cases), anisometropia (26%), and strabismus (56%).

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.

Most people with Bell's palsy start to regain normal facial function within 3 weeks—even those who do not receive treatment. In a 1982 study, when no treatment was available, of 1,011 patients, 85% showed first signs of recovery within 3 weeks after onset. For the other 15%, recovery occurred 3–6 months later. After a follow-up of at least 1 year or until restoration, complete recovery had occurred in more than two-thirds (71%) of all patients. Recovery was judged moderate in 12% and poor in only 4% of patients. Another study found that incomplete palsies disappear entirely, nearly always in the course of one month. The patients who regain movement within the first two weeks nearly always remit entirely. When remission does not occur until the third week or later, a significantly greater part of the patients develop sequelae. A third study found a better prognosis for young patients, aged below 10 years old, while the patients over 61 years old presented a worse prognosis.

Major complications of the condition are chronic loss of taste (ageusia), chronic facial spasm, facial pain and corneal infections. To prevent the latter, the eyes may be protected by covers, or taped shut during sleep and for rest periods, and tear-like eye drops or eye ointments may be recommended, especially for cases with complete paralysis. Where the eye does not close completely, the blink reflex is also affected, and care must be taken to protect the eye from injury.

Another complication can occur in case of incomplete or erroneous regeneration of the damaged facial nerve. The nerve can be thought of as a bundle of smaller individual nerve connections that branch out to their proper destinations. During regrowth, nerves are generally able to track the original path to the right destination - but some nerves may sidetrack leading to a condition known as synkinesis. For instance, regrowth of nerves controlling muscles attached to the eye may sidetrack and also regrow connections reaching the muscles of the mouth. In this way, movement of one also affects the other. For example, when the person closes the eye, the corner of the mouth lifts involuntarily.

Around 9% of patients have some sort of sequelae after Bell's palsy, typically the synkinesis already discussed, or spasm, contracture, tinnitus and/or hearing loss during facial movement or crocodile tear syndrome. This is also called gustatolacrimal reflex or Bogorad's Syndrome and involves the sufferer shedding tears while eating. This is thought to be due to faulty regeneration of the facial nerve, a branch of which controls the lacrimal and salivary glands. Gustatorial sweating can also occur.

Alien hand syndrome (AHS) is a condition in which a person experiences their limbs acting seemingly on their own, without control over the actions. The term is used for a variety of clinical conditions and most commonly affects the left hand. There are many similar names used to describe the various forms of the condition but they are often used inappropriately. The afflicted person may sometimes reach for objects and manipulate them without wanting to do so, even to the point of having to use the controllable hand to restrain the alien hand. While under normal circumstances, thought, as intent, and action can be assumed to be deeply mutually entangled, the occurrence of alien hand syndrome can be usefully conceptualized as a phenomenon reflecting a functional "disentanglement" between thought and action.

Alien hand syndrome is best documented in cases where a person has had the two hemispheres of their brain surgically separated, a procedure sometimes used to relieve the symptoms of extreme cases of epilepsy and epileptic psychosis, e.g., temporal lobe epilepsy. It also occurs in some cases after brain surgery, stroke, infection, tumor, aneurysm, migraine and specific degenerative brain conditions such as Alzheimer's disease and Creutzfeldt–Jakob disease. Other areas of the brain that are associated with alien hand syndrome are the frontal, occipital, and parietal lobes.

"Alien behavior" can be distinguished from reflexive behavior in that the former is flexibly purposive while the latter is obligatory. Sometimes the sufferer will not be aware of what the alien hand is doing until it is brought to his or her attention, or until the hand does something that draws their attention to its behavior. There is a clear distinction between the behaviors of the two hands in which the affected hand is viewed as "wayward" and sometimes "disobedient" and generally out of the realm of their own voluntary control, while the unaffected hand is under normal volitional control. At times, particularly in patients who have sustained damage to the corpus callosum that connects the two cerebral hemispheres (see also split-brain), the hands appear to be acting in opposition to each other.

A related syndrome described by the French neurologist François Lhermitte involves the release through disinhibition of a tendency to compulsively utilize objects that present themselves in the surrounding environment around the patient. The behavior of the patient is, in a sense, obligatorily linked to the "affordances" (using terminology introduced by the American ecological psychologist, James J. Gibson) presented by objects that are located within the immediate peri-personal environment.

This condition, termed "utilization behavior", is most often associated with extensive bilateral frontal lobe damage and might actually be thought of as "bilateral" alien hand syndrome in which the patient is compulsively directed by external environmental contingencies (e.g. the presence of a hairbrush on the table in front of them elicits the act of brushing the hair) and has no capacity to "hold back" and inhibit pre-potent motor programs that are obligatorily linked to the presence of specific external objects in the peri-personal space of the patient. When the frontal lobe damage is bilateral and generally more extensive, the patient completely loses the ability to act in a self-directed manner and becomes totally dependent upon the surrounding environmental indicators to guide his behavior in a general social context, a condition referred to as "environmental dependency syndrome".

In order to deal with the alien hand, some patients engage in personification of the affected hand. Usually these names are negative in nature, from mild such as "cheeky" to malicious "monster from the moon". For example, Doody and Jankovic described a patient who named her alien hand "baby Joseph". When the hand engaged in playful, troublesome activities such as pinching her nipples (akin to biting while nursing), she would experience amusement and would instruct baby Joseph to "stop being naughty". Furthermore, Bogen suggested that certain personality characteristics, such as a flamboyant personality, contribute to frequent personification of the affected hand.

Neuroimaging and pathological research shows that the frontal lobe (in the frontal variant) and corpus callosum (in the callosal variant) are the most common anatomical lesions responsible for the alien hand syndrome. These areas are closely linked in terms of motor planning and its final pathways.

The callosal variant includes advanced willed motor acts by the non-dominant hand, where patients frequently exhibit "intermanual conflict" in which one hand acts at cross-purposes with the other "good hand". For example, one patient was observed putting a cigarette into her mouth with her intact, "controlled" hand (her right, dominant hand), following which her alien, non-dominant, left hand came up to grasp the cigarette, pull the cigarette out of her mouth, and toss it away before it could be lit by the controlled, dominant, right hand. The patient then surmised that "I guess 'he' doesn't want me to smoke that cigarette." Another patient was observed to be buttoning up her blouse with her controlled dominant hand while the alien non-dominant hand, at the same time, was unbuttoning her blouse. The frontal variant most often affects the dominant hand, but can affect either hand depending on the lateralization of the damage to medial frontal cortex, and includes grasp reflex, impulsive groping toward objects or/and tonic grasping (i.e. difficulty in releasing grip).

In most cases, classic alien-hand signs derive from damage to the medial frontal cortex, accompanying damage to the corpus callosum. In these patients the main cause of damage is unilateral or bilateral infarction of cortex in the territory supplied by the anterior cerebral artery or associated arteries. Oxygenated blood is supplied by the anterior cerebral artery to most medial portions of the frontal lobes and to the anterior two-thirds of the corpus callosum, and infarction may consequently result in damage to multiple adjacent locations in the brain in the supplied territory. As the medial frontal lobe damage is often linked to lesions of the corpus callosum, frontal variant cases may also present with callosal form signs. Cases of damage restricted to the callosum however, tend not to show frontal alien-hand signs.

Conditions that can cause disfigurement include:

- severe acne

- acromegaly

- amniotic band constriction

- amputation

- argyria

- birthmarks

- burns

- cancer

- cataracts

- circumcision

- cleft lip

- eczema

- elephantiasis

- erysipelas

- gangrene

- gigantomastia

- gynecomastia

- keloids

- leprosy

- necrosis

- McCune–Albright syndrome

- neurofibromatosis

- noma

- paralysis

- proteus syndrome

- radiation poisoning

- scalping

- scars

- smallpox

- severe strabismus

- synkinesis

- Syphilis

- vitiligo

- severe warts

Plastic surgery or reconstructive surgery is available in many cases to disfigured people. Some health insurance companies and government health care systems cover plastic surgery for these problems when they do not generally cover plastic surgery for what is labeled as "cosmetic purposes".

The term "disfigurement" is sometimes used pejoratively to describe the results of intentional body modification. Scarification and other forms of such modification will sometimes be referred to as such by neutral parties or by advocates of the processes as well. Many types of body modification are subject to strong social debate as such.

Disfigurement, whether caused by a benign or malignant condition, often leads to severe psychosocial problems such as negative body image; depression; difficulties in one's social, sexual, and professional lives; prejudice; and intolerance. This is partly due to how the individual copes with looking 'visibly different', though the extent of the disfigurement rarely correlates with the degree of distress the sufferer feels. An additional factor which affects sufferers of a disfigurement is the reaction they get from other people. Studies have shown that the general population respond to people with a disfigurement with less trust, less respect and often try to avoid making contact or having to look at the disfigurement. Disfigurements affecting visible areas such as the face, arms and hands are thought to present greater difficulty for sufferers to cope with than do other disfigurements.

Deliberate mutilation resulting in physical disfigurement has also been practiced by many cultures throughout human history for religious or judicial purposes. During the Byzantine Empire, the emperor was considered God's on Earth, and as such the physical wholeness of his person was an essential complement to the perfection of Heaven. For this reason, many deposed emperors were blinded, had their noses cut off, or their tongue split by their successors, as these permanent disfigurements disqualified them from ever reclaiming the throne.

A case of voluntary disfigurement is that of St. Æbbe the Younger and the nuns of Coldingham Monastery in Scotland. When the monastery was attacked by Vikings and they feared being raped, she and the nuns cut off their own noses and upper lips. In revenge, the Vikings burned down the building with the nuns inside. This is said to be the origin of the phrase "cutting off the nose to spite the face".

IHH is divided into two syndromes: IHH with olfactory alterations or anosmia, Kallmann syndrome and IHH with normal smell (normosmic IHH).

Kallmann syndrome is responsible for approximately 50% of all cases of the condition. It is associated with mutations in "KAL1", "FGFR1/FGF8", "FGF17", "IL17RD", "PROKR2", "NELF", "CHD7"(which positively regulates GnRH secretion), HS6ST1, "FLRT3", "SPRY4", DUSP6, "SEMA3A", and "WDR11 (gene)", genes which are related to defects in neuronal migration.

Gene defects associated with IHH and normal smell include "PROKR2, FGFR1, FGF8, CHD7, DUSP6," and "WDR11", as in KS, but in addition

also mutations in "KISS1R", "TACR3", GNRH1/GNRHR, LEP/LEPR, HESX1, FSHB, and LHB.

GnRH insensitivity is the second most common cause of IHH, responsible for up to 20% of cases.

A minority of less than 5-10% is due to inactivating mutations in genes which positively regulate GnRH secretion such as ,"CHD7", "KISS1R", and "TACR3".

The causes of about 25% of all IHH cases are still unknown.

Isolated hypogonadotropic hypogonadism (IHH), also called idiopathic or congenital hypogonadotropic hypogonadism (CHH), as well as isolated or congenital gonadotropin-releasing hormone deficiency (IGD) constitutes a small subset of cases of hypogonadotropic hypogonadism (HH).

IHH is due to deficiency in or insensitivity to gonadotropin-releasing hormone (GnRH), where the function and anatomy of the anterior pituitary is otherwise normal, and secondary causes of HH are not present.

Isolated hypogonadotropic hypogonadism (IHH), also called idiopathic or congenital hypogonadotropic hypogonadism (CHH), as well as isolated or congenital gonadotropin-releasing hormone deficiency (IGD), is a condition which results in a small subset of cases of hypogonadotropic hypogonadism (HH) due to deficiency in or insensitivity to gonadotropin-releasing hormone (GnRH) where the function and anatomy of the anterior pituitary is otherwise normal and secondary causes of HH are not present.