Macroglossia is usually diagnosed clinically. Sleep endoscopy and imaging may be used for assessment of obstructive sleep apnea. The initial evaluation of all patients with macroglossia may involve abdominal ultrasound and molecular studies for Beckwith–Wiedemann syndrome.

A clinical diagnosis of SCS can be verified by testing the TWIST1 gene (only gene in which mutations are known to cause SCS) for mutations using DNA analysis, such as sequence analysis, deletion/duplication analysis, and cytogenetics/ FISH analysis. Sequence analysis of exon 1 (TWIST1 coding region) provides a good method for detecting the frequency of mutations in the TWIST1 gene. These mutations include nonsense, missense, splice site mutation, and intragenic deletions/insertions. Deletion/duplication analysis identifies mutations in the TWIST1 gene that are not readily detected by sequence analysis. Common methods include PCR, multiplex ligation-dependent probe amplification (MLPA), and chromosomal microarray (CMA). Cytogenetic/FISH analysis attaches fluorescently labels DNA markers to a denatured chromosome and is then examined under fluorescent lighting, which reveals mutations caused by translocations or inversions involving 7p21. Occasionally, individuals with SCS have a chromosome translocation, inversion, or ring chromosome 7 involving 7p21 resulting in atypical findings, such as, increased developmental delay. Individuals with SCS, typically have normal brain functioning and rarely have mental impairments. For this reason, if an individual has both SCS and mental retardation, then they should have their TWIST1 gene screened more carefully because this is not a normal trait of SCS. Cytogenetic testing and direct gene testing can also be used to study gene/chromosome defects. Cytogenetic testing is the study of chromosomes to detect gains or losses of chromosomes or chromosome segments using fluorescent in situ hybridization (FISH) and/or comparative genomic hybridization (CGH). Direct gene testing uses blood, hair, skin, amniotic fluid, or other tissues in order to find genetic disorders. Direct gene testing can determine whether an individual has SCS by testing the individual's blood for mutations in the TWIST1 gene.

Up until recently, experts frequently disagreed on whether a patient had SCS, Crouzon syndrome, isolated craniosynostosis, or some other disease because the symptoms are so closely related, they literally had no way of differentiating between all of them. However, we now have direct gene testing, which allows for a more definitive diagnosis because it allows them to be differentiated from each other based on which gene is mutated in each condition. The following is a list of conditions commonly confused/misdiagnosed for SCS, some of their symptoms, and which mutated gene each contains:

Current research is focusing on clearly defining the phenotype associated with tetrasomy 18p and identifying which genes cause medical and developmental problems when present in four copies.

Suspicion of a chromosome abnormality is typically raised due to the presence of developmental delays or congenital malformations. Diagnosis of tetrasomy 18p is typically made via a routine chromosome analysis from a blood sample. The diagnosis can also be made prenatally by chorionic villus sampling or amniocentesis.

Severity of tetrasomy 18p is variable. Individuals with mosaicism are typically less severely affected than non-mosaic individuals.

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.

This condition can be diagnosed by genetic testing. Furthermore, an echocardiogram and X-ray may help in the diagnosis.

Additional findings that may be present in HFGS according to the latest research are:

- Limited metacarpophalangeal flexion of the thumb or limited ability to oppose the thumb and fifth finger

- Hypoplastic thenar eminences

- Medial deviation of the great toe (hallux varus), a useful diagnostic sign when present

- Small great toenail

- Fifth-finger clinodactyly, secondary to a shortened middle phalanx

- Short feet

- Altered dermatoglyphics of the hands; when present, primarily involving distal placement of the axial triradius, lack of thenar or hypothenar patterning, low arches on the thumbs, thin ulnar loops (deficiency of radial loops and whorls), and a greatly reduced ridge count on the fingers

Radiographic findings

- Hypoplasia of the distal phalanx and first metacarpal of the thumbs and great toes

- Pointed distal phalanges of the thumb

- Lack of normal tufting of the distal phalanges of the great toes

- Fusions of the cuneiform to other tarsal bones or trapezium-scaphoid fusion of the carpals

- Short calcaneus

- Occasional bony fusions of the middle and distal phalanges of the second, third, fourth, or fifth toes

- Delayed carpal or tarsal maturation

- Metacarpophalangeal profile reflecting shortening of the first metacarpal, the first and second phalanges, and the second phalanx of the second and fifth digits

Urogenital Defects

Females may have the following:

- Vesicoureteral reflux secondary to ureteric incompetence

- Ectopic ureteral orifices

- Trigonal hypoplasia

- Hypospadiac urethra

- Subsymphyseal epispadias

- Patulous urethra

- Urinary incontinence (related to structural anomalies and weakness of the bladder sphincter muscle)

- Small hymenal opening

- Various degrees of incomplete Müllerian fusion with or without two cervices or a longitudinal vaginal septum

Males may have the following:

- Retrograde ejaculation (related to structural anomalies and weakness of the bladder sphincter muscle)

Treatment and prognosis of macroglossia depends upon its cause, and also upon the severity of the enlargement and symptoms it is causing. No treatment may be required for mild cases or cases with minimal symptoms. Speech therapy may be beneficial, or surgery to reduce the size of the tongue (reduction glossectomy). Treatment may also involve correction of orthodontic abnormalities that may have been caused by the enlarged tongue. Treatment of any underlying systemic disease may be required, e.g. radiotherapy.

Even though clinical diagnostic criteria have not been 100 percent defined for genitopatellar syndrome, the researchers stated that the certain physical features could relate to KAT6B mutation and result in the molecular genetic testing. The researchers stated that the Individuals with two major features or one major feature and two minor features are likely to have a KAT6B mutation.

To diagnose the Genitopatellar Syndrome, there are multiple ways to evaluate.

Medical genetics consultation

- Evaluation by developmental specialist

- Feeding evaluation

- Baseline hearing evaluation

- Thyroid function tests

- Evaluation of males for cryptorchidism

- Orthopedic evaluation if contractures are present or feet/ankles are malpositioned

- Hip radiographs to evaluate for femoral head dislocation

- Renal ultrasound examination for hydronephrosis and cysts

- Echocardiogram for congenital heart defects

- Evaluation for laryngomalacia if respiratory issues are present

- Evaluation by gastroenterologist as needed, particularly if bowel malrotation is suspected

Evaluation of a child with torticollis begins with history taking to determine circumstances surrounding birth and any possibility of trauma or associated symptoms. Physical examination reveals decreased rotation and bending to the side opposite from the affected muscle. Some say that congenital cases more often involve the right side, but there is not complete agreement about this in published studies. Evaluation should include a thorough neurologic examination, and the possibility of associated conditions such as developmental dysplasia of the hip and clubfoot should be examined. Radiographs of the cervical spine should be obtained to rule out obvious bony abnormality, and MRI should be considered if there is concern about structural problems or other conditions.

Ultrasonography is another diagnostic tool that has high frequency sound waves used to visualize the muscle tissue. A colour histogram can also be used to determine cross sectional area and thickness of the muscle.

Evaluation by an optometrist or an ophthalmologist should be considered in children to ensure that the torticollis is not caused by vision problems (IV cranial nerve , nystagmus-associated "null position," etc.).

Differential diagnosis for torticollis involves

- Cranial nerve IV palsy

- Spasmus nutans

- Sandifer syndrome

- Myasthenia gravis

Cervical dystonia appearing in adulthood has been believed to be idiopathic in nature, as specific imaging techniques most often find no specific cause.

There is disagreement as to how cases of KTS should be classified if there is an arteriovenous fistula present. Although several authorities have suggested that the term Parkes-Weber syndrome is applied in those cases, ICD-10 currently uses the term "Klippel–Trénaunay–Weber syndrome".

The differential diagnosis of this condition consists of:

- Hypertrophic cardiomyopathy

- Beckwith-Wiedemann syndrome

- Berardinelli-Seip congenital lipodystrophy

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.

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

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.

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

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.

KTS is a complex syndrome, and no single treatment is applicable for everyone. Treatment is decided on a case-by-case basis with the individual's doctors.

At present, many of the symptoms may be treated, but there is no cure for Klippel–Trenaunay syndrome.

The key problem is the early fusion of the skull, which can be corrected by a series of surgical procedures, often within the first three months after birth. Later surgeries are necessary to correct respiratory and facial deformities.

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.

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.

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.

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.

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.