All people with this disorder have at least one limb abnormality that affects bones in the wrist (carpal bones). Often, these wrist bone abnormalities can be detected only by X-ray. Affected individuals may have additional bone abnormalities that can include polydactyly, a hypoplastic thumb or a Triphalangeal thumb, partial or complete absence of bones in the forearm, an underdeveloped Humerus, and abnormalities that affect the Clavicle and Scapula. Bone abnormalities may affect each arm differently, and the left side can be affected more than the right side. In some cases, only one arm and/or hand is affected.

About 75 percent of individuals with Holt–Oram syndrome have heart problems. The most common problem is a defect in the muscular wall, or septum, that separates the right and left sides of the heart (atria). Atrial septal defects (ASD) are caused by a hole in the septum between the left and right upper chambers of the heart (atria), and ventricular septal defects (VSD) are caused by a hole in the septum between the left and right lower chambers of the heart (ventricles). Sometimes people with Holt–Oram syndrome have cardiac conduction disease, which is caused by abnormalities in the electrical system that coordinates contractions of the heart chambers. Cardiac conduction disease can lead to problems such as a slow heart rate (bradycardia) or a rapid and ineffective contraction of the heart muscles (fibrillation). Cardiac conduction disease can occur along with other heart defects (such as septal defects) or as the only heart problem in people with Holt–Oram syndrome.

It involves numerous anomalies including:

- Post-axial polydactyly

- Congenital heart defects (most commonly an atrial septal defect producing a common atrium, occurring in 60% of affected individuals)

- Teeth present at birth (natal teeth)

- Fingernail dysplasia

- Short-limbed dwarfism, mesomelic pattern

- Short ribs

- Cleft palate

- Malformation of the wrist bones (fusion of the hamate and capitate bones).

Holt–Oram syndrome (also called Heart and Hand Syndrome, atrio-digital syndrome, atriodigital dysplasia, cardiac-limb syndrome, heart-hand syndrome type 1, HOS, ventriculo-radial syndrome) is an autosomal dominant disorder that affects bones in the arms and hands (the upper limbs) and may also cause heart problems. The syndrome includes an absent radial bone in the arms, an atrial septal defect, and a first degree heart block. Thalidomide syndrome can produce similar morphology to Holt–Oram syndrome, sufficient to be considered a phenocopy.

Ectrodactyly involves the deficiency or absence of one or more central digits of the hand or foot and is also known as split hand–split foot malformation (SHFM). The hands and feet of people with ectrodactyly are often described as "claw-like" and may include only the thumb and one finger (usually either the little finger, ring finger, or a syndactyly of the two) with similar abnormalities of the feet.

Ectodermal dysplasia describes abnormalities of structures derived from the embryonic ectoderm. These abnormalities affect both the superficial ectodermal layer, as well as the mesectodermal layer constituted by the neural crest.

There is a range of signs and symptoms including cleft lip or palate, mental retardation and various forms of ectodermal dysplasia. Additional symptoms may include fused eyelids, absent nails, delayed bone growth and dry skin. It is believed that this syndrome follows an autosomal dominant pattern of inheritance with incomplete penetrance, and caused by a mutation affecting the TP63 gene. It has been suggested that this syndrome, AEC syndrome and Rapp–Hodgkin syndrome may be variations of the same disease.

Ectodermal dysplasia is characterized by absent sweat glands resulting in dry (hypohydrotic), often scale-like skin, sparse and usually coarse scalp hair that is often blonde, sparse eyebrows and eyelashes, and small brittle nails. In addition, abnormalities of ectodermal derivatives, neuroectodermal derivatives, and mesectodermal derivatives are often found. The ectodermal derivative abnormalities can affect the epidermis including mammary, pituitary and sweat glands, as well as hairs, dental enamel, nails, lens, and the internal ear. Neuroectodermal derivatives that can be affected include sensory placodes, cutaneous pigmental cells, and hair buds. Mesectodermal derivatives affected can include the dermis, hypodermis, dentin, head muscles and conjunctival cells, cervicofacial vascular endothelial cells, and part of the maxillofacial skeleton.

The hypohydrotic symptoms of ectodermal dysplasia described above are evidenced not only in the skin of affected individuals, but also in their phonation and voice production. Because the vocal folds may not be as hydrated as is necessary during the adduction phase of vocal fold vibration (due to lack of lubrication), a complete seal may not be accomplished between the folds and mucosal wave movement may be disrupted. This results in air escapement between the folds and the production of breathy voice, which often accompanies the skin abnormalities of ectodermal dysplasia.

There is no specific treatment or cure for individuals affected with this type of syndrome, though some of the abnormal physical features may be surgically correctable.

People with ODD syndrome often have a characteristic appearance. Visible features of the condition include:

- small teeth that are prone to caries because of underdeveloped tooth enamel;

- a long, thin nose;

- unusually small eyes; and

- type III syndactyly of the fourth and fifth fingers.

Iris atrophy and glaucoma are more common than average. The size of the eyes often interferes with learning to read; special eyeglasses may be required. Hair may be fine, thin, dry, or fragile; in some families, it is curly.

Neurologic abnormalities may be seen in adults. The neurologic changes may appear earlier in each subsequent generation and can include abnormal white matter, conductive deafness, and various kinds of paresis, including ataxia, spastic paraplegia, difficulty controlling the eyes, and bladder and bowel disturbances.

ADULT syndrome features include ectrodactyly, syndactyly, excessive freckling, lacrimal duct anomalies, dysplastic nails, hypodontia, hypoplastic breasts and nipples, hypotrichosis, hypohidrosis, broad nasal bridge, midfacial hypoplasia, exfoliative dermatitis, and xerosis. The lack of facial clefting and ankyloblepharon are important because they exist in ectrodactyly–ectodermal dysplasia–cleft syndrome (EEC) but not in ADULT syndrome.

RL syndrome is characterized by renal dysplasia, growth retardation, phocomelia or mesomelia, radiohumeral fusion (joining of radius and humerus), rib abnormalities, anomalies of the external genitalia and potter-like facies among many others.

Acro–dermato–ungual–lacrimal–tooth (ADULT) syndrome is a rare genetic disease. ADULT syndrome is an autosomal dominant form of ectodermal dysplasia, a group of disorders that affects the hair, teeth, nails, sweat glands, and extremities. The syndrome arises from a mutation in the TP63 gene. This disease was previously thought to be a form of ectrodactyly–ectodermal dysplasia–cleft syndrome (EEC), but was classified as a different disease in 1993 by Propping and Zerres.

In HWS the hair is coarse and sparse, eyelashes are sparse or absent, nails may be absent or malformed, and teeth may be small and malformed. There may be fewer than normal sweat glands and they may produce little sweat, a condition known generally as hypohidrosis. Chronic inflammatory dermatitis of the scalp is a common symptom.

Two features differentiate HWS from other ectodermal displasias. First, the syndrome is associated with cleft palate, and, less often, cleft lip. Second, the edges of the upper and lower eyelid grow bands of fibrous tissue, often causing them to be fused together. This condition in the eyelids is called "ankyloblepharon filiforme adnatum".

Renal dysplasia-limb defects syndrome (RL syndrome), also known as Ulbright–Hodes syndrome, is a very rare autosomal recessive congenital disorder. It has been described in three infants, all of whom died shortly after birth.

Ellis–van Creveld Syndrome (also called "chondroectodermal dysplasia" or "mesoectodermal dysplasia" but see 'Nomenclature' section below) is a rare genetic disorder of the skeletal dysplasia type.

Individuals affected by an ED syndrome frequently have abnormalities of the hair follicles. Scalp and body hair may be thin, sparse, and very light in color, even though beard growth in affected males may be normal. The hair may grow very slowly or sporadically and it may be excessively fragile, curly, or even twisted.

Oculodentodigital syndrome (ODD syndrome) is an extremely rare genetic condition that typically results in small eyes, underdeveloped teeth, and syndactyly and malformation of the fourth and fifth fingers. It has also been called oculo-dento-digital syndrome, oculodentodigital dysplasia (ODDD), and oculodentoosseous dysplasia (ODOD). It is considered a kind of ectodermal dysplasia.

It is an autosomal recessive disorder in which mild clinical manifestations contrast with radiological appearances of gross metaphyseal undermodeling. Most patients present with mild genu valgum. The elbows are unable to extend fully. There may be widening of the lower femora and clavicles. Bones can sometimes be fragile, but fracturing is usually not common. Patients may present with dental caries, mandibular prognathism, spinal alignment, and disproportionate limb lengthening. Mental development, physical development, and height are usually normal.

The optic nerve hypoplasia is generally manifested by nystagmus (involuntary eye movements, often side-to-side) and a smaller-than-usual optic disc. The degree of visual impairment is variable, and ranges from normal vision to complete blindness. When nystagmus develops, it typically appears by 1–8 months of age, and usually indicates that there will be a significant degree of visual impairment, but the severity is difficult to predict in infancy. Although there are many measures to compensate for visual impairment, there are few treatments available to induce normal optic nerve function.

Pyle disease may be confused with craniometaphyseal dysplasia. The two, however, are clinically, radiographically, and genetically distinct from one another.

Hay–Wells syndrome (also known as AEC syndrome; see "Naming") is one of at least 150 known types of ectodermal dysplasia.These disorders affect tissues that arise from the ectodermal germ layer, such as skin, hair, and nails.

The degree of pituitary deficiency is also variable, and ranges from normal function, to deficiency of both anterior and posterior hormones. It is often unclear if the hypopituitarism is due to a primary pituitary dysfunction or is secondary to a hypothalamic dysfunction. Hypopituitarism in this syndrome is most often manifested by growth hormone deficiency. If severe, it can lead to diagnosis in the first days of life by causing hypoglycemia, jaundice, and micropenis (if a boy). The cause of the jaundice is unknown, and an unusual aspect of it (compared to most neonatal jaundice) is that it can be largely a conjugated (direct) hyperbilirubinemia suggestive of obstructive liver disease. It typically resolves over several weeks once hormone replacement is begun. All of the pituitary hormones can be replaced, and this is the treatment for deficiencies. Septo-optic dysplasia is one of the most common forms of congenital growth hormone deficiency.

Fingernails and toenails may be thick, abnormally shaped, discolored, ridged, slow-growing, or brittle. The cuticles may be prone to infections.

This condition is also characterized by an unusual clubfoot with twisting of the metatarsals, inward- and upward-turning foot, tarsus varus, and inversion adducted appearances. Furthermore, they classically present with scoliosis (progressive curvature of the spine), and unusually positioned thumbs (hitchhiker thumbs). About half of infants with diastrophic dysplasia are born with an opening in the roof of the mouth called a cleft palate. Swelling of the external ears is also common in newborns and can lead to thickened, deformed ears.

The signs and symptoms of diastrophic dysplasia are similar to those of another skeletal disorder called atelosteogenesis, type 2; however diastrophic dysplasia tends to be less severe.

People with this condition are short-statured from birth, with a very short trunk and shortened limbs. Their hands and feet, however, are usually average-sized. Curvature of the spine (scoliosis and lumbar lordosis) may be severe and can cause problems with breathing. Changes in the spinal bones (vertebrae) in the neck may also increase the risk of spinal cord damage. Other skeletal signs include flattened vertebrae (platyspondyly), severe protrusion of the breastbone (pectus carinatum), a hip joint deformity in which the upper leg bones turn inward (coxa vara), and a foot deformity known as clubfoot.

Affected individuals have mild and variable changes in their facial features. The cheekbones close to the nose may appear flattened. Some infants are born with an opening in the roof of the mouth, which is called a cleft palate. Severe nearsightedness (high myopia) and detachment of the retina (the part of the eye that detects light and color) are also common.

This condition is a skeletal dysplasia characterized by short stature, mild brachydactyly, kyphoscoliosis, abnormal gait, enlarged knee joints, precocious osteoarthropathy, platyspondyly, delayed epiphyseal ossification, mild metaphyseal abnormalities, short stature and short and bowed legs. Intelligence is normal.

Some patients may manifest premature pubarche and hyperandrogenism.

Other features that may form part of the syndrome include precocious costal calcification, small iliac bones, short femoral necks, coxa vara, short halluces and fused vertebral bodies.