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.

Hand-foot-genital syndrome is inherited in an autosomal dominant manner. The proportion of cases caused by de novo mutations is unknown because of the small number of individuals described. If a parent of the proband is affected, the risk to the siblings is 50%. When the parents are clinically unaffected, the risk to the sibs of a proband appears to be low. Each child of an individual with HFGS has a 50% chance of inheriting the mutation. Prenatal testing may be available through laboratories offering custom prenatal testing for families in which the disease-causing mutation has been identified in an affected family member.

It is a feature of Turner syndrome (only found in girls) and Noonan syndrome, as well as the rarer Klippel-Feil syndrome, or Diamond-Blackfan Anemia

Macroglossia is uncommon, and usually occurs in children. Macroglossia has been reported to have a positive family history in 6% of cases. The National Organization of Rare Disorders lists macroglossia as a rare disease (less than 200 000 individuals in the US).

Congenital hypertrophy of the lateral fold of the hallux is a rare cutaneous condition of unknown pathology that present to newborns. The condition was "first described by Martinet et al. in 1984." This sometimes painful condition involves "an overgrowth of the soft tissue" that can partially cover the nail plate. The condition usually effects both extremities and the condition can later reverse spontaneously.

On babies, webbed neck may look like loose folds of skin on the neck. As the child grows, the skin may stretch out to look like there is little or no neck.

Diagnosis is based on physical examination including radiographs of the hands and feet and imaging studies of the kidneys, bladder, and female reproductive tract. HOXA13 is the only gene known to be associated with HFGS. Approximately 60% of mutations are polyalanine expansions. Molecular genetic testing is clinically available.

Females are affected more than males, and the condition occurs in permanent (adult) teeth more than deciduous (baby teeth or milk teeth).

SCS is the most common craniosynostosis syndrome and affects 1 in every 25,000 to 50,000 individuals. It occurs in all racial and ethnic groups, and affects males and females equally. If a parent carries a copy of the SCS gene mutation, then there is a 50% chance their child will also carry a copy of the gene mutation, in which case, the child may or may not show signs of SCS. There is also a 50% chance their child will have two working copies of the gene, and would therefore, not have SCS. If both parents carry a single copy of the SCS gene mutation, then there is a 25% chance their child will have two gene mutation copies (so child would develop severe SCS), a 25% chance their child would have two normal copies of the gene (so would be completely normal), and a 50% chance their child would carry one gene mutation copy and 1 normal copy (so child may or may not display SCS). In rare situations, two normal parents can have a child with SCS due to a "de novo" mutation. The exact cause of the "de novo" mutation is unknown, but it doesn't seem to be related to anything that the parents did or didn't do during the pregnancy. SCS due to a "de novo" mutation is so rare that the proportion of past cases is unknown.

Fibular hemimelia or longitudinal fibular deficiency is "the congenital absence of the fibula and it is the most common congenital absence of long bone of the extremities." It is the shortening of the fibula at birth, or the complete lack thereof. In humans, the disorder can be noted by ultrasound in utero to prepare for amputation after birth or complex bone lengthening surgery. The amputation usually takes place at six months with removal of portions of the legs to prepare them for prosthetic use. The other treatments which include repeated corrective osteotomies and leg-lengthening surgery (Ilizarov apparatus) are costly and associated with residual deformity.

Severe congenital onychogryphosis affecting all twenty nailbeds has been recorded in two families who exhibit the dominant allele for a certain gene. Congenital onychogryphosis of the fifth toe (the little toe) is fairly common, but asymptomatic and seldom brought to the attention of medical professionals. Rather, it is brought to the attention of manicurists who routinely file the clawed toenail flat.

Some recommend avulsion of the nail plate with surgical destruction of the nail matrix with phenol or the carbon dioxide laser, if the blood supply is good.

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.

The birth defect affects men and women equally, and is not limited to any racial group. It is not certain if it is genetic in nature, although testing is ongoing. There is some evidence that it may be associated with a translocation at t(8;14)(q22.3;q13). Some researchers have suggested AGGF1 has an association.

There are many potential factors involved.

- Congenital hypopituitarism

- Ectodermal dysplasia

- Down syndrome

- Ionizing radiation to the jaws during tooth development (odontogenesis)

- Chemotherapy during tooth development

- Marshall syndrome

- Rieger syndrome

- Focal dermal hypoplasia

- Silver-Russell syndrome

- Williams syndrome

- Gorlin-Chaudhry-Moss syndrome

- Coffin–Siris syndrome

- Salamon syndrome

- Cleft lip and palate

Others include trichorhinopharyngeal, odontotrichomelic, neuroectodermal and dermo-odontodysplasia syndromes.

Prosthetic replacement of missing teeth is possible using dental implant technology or dentures. This treatment can be successful in giving patients with anodontia a more aesthetically pleasing appearance. The use of an implant prosthesis in the lower jaw could be recommended for younger patients as it is shown to significantly improve the craniofacial growth, social development and self-image. The study associated with this evidence worked with individuals who had ectodermal dysplasia of varying age groups of up to 11, 11 to 18 and more than 18 years. It was noted that the risk of implant failure was significantly higher in patients younger than 18 years, but there is significant reason to use this methodology of treatment in those older. Overall the use of an implant-prosthesis has a considerable functional, aesthetic and psychological advantage when compared to a conventional denture, in the patients.

Three main support groups of this syndrome are the ASGA in Australia, The Association for Children with Genetic Disorders in Poland, and the Association of People of Genetic Disorders in Greece.

Epicanthic folds appear in East Asians, Southeast Asians, Central Asians, North Asians, some South Asians, Polynesians, Micronesians, Indigenous Americans (as well as Mestizos), the Khoisan, Malagasy, occasionally Europeans (e.g., Scandinavians, Hungarians, Samis, Irish and Poles) and among Nilotes.

Anthropologist Carleton S. Coon states that the "median fold" occurs in Finnic and Slavic populations, while the "true inner or mongoloid fold" appears in populations of the east and the far north.

Prenatal diagnosis of Saethre-Chotzen Syndrome in high risk pregnancies is doable, but very uncommon and rarely performed. Furthermore, this is only possible if the mutation causing the disease has already been identified within the family genome. There are a few different techniques in which prenatal testing can be carried out. Prenatal testing is usually performed around 15–18 weeks, using amniocentesis to extract DNA from the fetus's cells. Prenatal testing can also be performed during weeks 10-12 using chorionic villus sampling (CVS) to extract DNA from the fetus. Recently, there has been an increased interest in utilizing ultrasound equipment in order to detect fetal skull abnormalities due to immature fusion of the cranial sutures.

Macroglossia may be caused by a wide variety of congenital and acquired conditions. Isolated macroglossia has no determinable cause. The most common causes of tongue enlargement are vascular malformations (e.g. lymphangioma or hemangioma) and muscular hypertrophy (e.g. Beckwith–Wiedemann syndrome or hemihyperplasia). Enlargement due to lymphangioma gives the tongue a pebbly appearance with multiple superficial dilated lymphatic channels. Enlargement due to hemihyperplasia is unilateral. In edentulous persons, a lack of teeth leaves more room for the tongue to expand into laterally, which can create problems with wearing dentures and may cause pseudomacroglossia.

Amyloidosis is an accumulation of insoluble proteins in tissues that impedes normal function. This can be a cause of macroglossia if amyloid is deposited in the tissues of the tongue, which gives it a nodular appearance. Beckwith–Wiedemann syndrome is a rare hereditary condition, which may include other defects such as omphalocele, visceromegaly, gigantism or neonatal hypoglycemia.

The tongue may show a diffuse, smooth generalized enlargement. The face may show maxillary hypoplasia causing relative mandibular prognathism. Apparent macroglossia can also occur in Down syndrome. The tongue has a papillary, fissured surface. Macroglossia may be a sign of hypothyroid disorders.

Other causes include mucopolysaccharidosis, neurofibromatosis, multiple endocrine neoplasia type 2B, myxedema, acromegaly, angioedema, tumors (e.g. carcinoma), Glycogen storage disease type 2, Simpson-Golabi-Behmel syndrome, Triploid Syndrome, trisomy 4p, fucosidosis, alpha-mannosidosis, Klippel-Trenaunay-Weber syndrome, cardiofaciocutaneous syndrome, Ras pathway disorders, transient neonatal diabetes, and lingual thyroid.

Children with Pfeiffer syndrome types 2 and 3 "have a higher risk for neurodevelopmental disorders and a reduced life expectancy" than children with Pfeiffer syndrome type 1, but if treated, favorable outcomes are possible. In severe cases, respiratory and neurological complications often lead to early death.

Epiblepharon is characterised by a congenital horizontal fold of skin near the margin of the upper or lower eyelid caused by the abnormal insertion of muscle fibres. This extra fold of skin redirects the lashes into a vertical position, where they may contact the globe. This is found most commonly in Asian individuals, especially children.

Many fetuses lose their epicanthic folds after three to six months of gestation.

Surgical excision is common and is a very effective mode of treatment.

In dentistry, anodontia, also called anodontia vera, is a rare genetic disorder characterized by the congenital absence of all primary or permanent teeth. It is associated with the group of skin and nerve syndromes called the ectodermal dysplasias. Anodontia is usually part of a syndrome and seldom occurs as an isolated entity.

Congenital absence of permanent teeth can present as hypodontia, usually missing 1 or 2 permanent teeth, or oligodontia that is the congenital absence of 6 or more teeth. Congenital absence of all wisdom teeth, or third molars, is relatively common. Anodontia is the congenital absence of teeth and can occur in some or all teeth (partial anodontia or hypodontia), involve two dentitions or only teeth of the permanent dentition (Dorland's 1998). Approximately 1% of the population suffers from oligodontia. Many denominations are attributed to this anomaly: partial anodontia, hypodontia, oligodontia, the congenital absence, anodontia, bilateral aplasia. Anodontia being the term used in controlled vocabulary Medical Subject Headings (MeSH) from MEDLINE which was developed by the United States National Library of Medicine. The congenital absence of at least one permanent tooth is the most common dental anomaly and may contribute to masticator dysfunction, speech impairment, aesthetic problems, and malocclusion (Shapiro and Farrington 1983). Absence of lateral incisors represents a major stereotype. Individuals with this condition are perceived as socially most aggressive compared with people without anodontia (Shaw 1981).