People with Aarskog-Scott syndrome often have distinctive facial features, such as widely spaced eyes (hypertelorism), a small nose, a long area between the nose and mouth (philtrum), and a widow's peak hairline. They frequently have mild to moderate short stature during childhood, but their growth usually catches up with that of their peers during puberty. Hand abnormalities are common in this syndrome and include short fingers (brachydactyly), curved pinky fingers (fifth finger clinodactyly), webbing of the skin between some fingers (cutaneous syndactyly), and a single crease across the palm. Other abnormalities in people with Aarskog-Scott syndrome include heart defects and a split in the upper lip (cleft lip) with or without an opening in the roof of the mouth (cleft palate).

Most males with Aarskog-Scott syndrome have a shawl scrotum, in which the scrotum surrounds the penis instead of hanging below. Less often, they have undescended testes (cryptorchidism) or a soft out-pouching around the belly-button (umbilical hernia) or in the lower abdomen (inguinal hernia).

The intellectual development of people with Aarskog-Scott syndrome varies widely. Some may have mild learning and behavior problems, while others have normal intelligence. In rare cases, severe intellectual disability has been reported.

Aarskog–Scott syndrome is a rare disease inherited as X-linked and characterized by short stature, facial abnormalities, skeletal and genital anomalies. This condition mainly affects males, although females may have mild features of the syndrome.

The Aarskog–Scott syndrome (AAS) is also known as the Aarskog syndrome, faciodigitogenital syndrome, shawl scrotum syndrome and faciogenital dysplasia.

In humans, a single transverse palmar crease is a single crease that extends across the palm of the hand, formed by the fusion of the two palmar creases (known in palmistry as the "heart line" and the "head line") and is found in people with Down Syndrome. It is also found in 1.5% of the general population in at least one hand.

Because it resembles the usual condition of non-human simians, it is also known as a simian crease or simian line, although these terms have widely fallen out of favor due to their pejorative connotation.

Shawl scrotum is a condition in which the scrotum surrounds the penis, resembling a 'shawl'.

It is a characteristic of some syndromes such as Aarskog-Scott syndrome (faciodigitogenital syndrome), Rubenstein-Taybi syndrome, craniofrontonasal dysplasia, Hunter Carpenter McDonald Syndrome, Naguib Syndrome, Saito Kuba Tsuruta Syndrome, Ieshima Koeda Inagaki syndrome, Cystic fibrosis Gastritis Megaloblastic Anemia, Willems de Vries syndrome, Schinzel syndrome and Seaver Cassidy syndrome.

Males are twice as likely as females to have this characteristic, and it tends to run in families. In its non-symptomatic form, it is more common among Asians and Native Americans than among other populations, and in some families there is a tendency to inherit the condition unilaterally, that is, on one hand only.

The presence of a single transverse palmar crease can be, but is not always, a symptom associated with abnormal medical conditions, such as fetal alcohol syndrome, or with genetic chromosomal abnormalities, including Down Syndrome (chromosome 21), cri du chat syndrome (chromosome 5), Klinefelter syndrome, Wolf-Hirschhorn Syndrome, Noonan syndrome (chromosome 12), Patau syndrome (chromosome 13), IDIC 15/Dup15q (chromosome 15), Edward's syndrome (chromosome 18), and Aarskog-Scott syndrome (X-linked recessive), or autosomal recessive disorder, such as Leaukocyte adhesion deficiency-2 (LAD2). A unilateral single palmar crease was also reported in a case of chromosome 9 mutation causing Nevoid basal cell carcinoma syndrome and Robinow syndrome. It is also sometimes found on the hand of the affected side of patients with Poland Syndrome, and craniosynostosis.

There is no consensus on what degree of angulation justifies a diagnosis, an incline between 15° and 30° is typical. A similar-sounding term, camptodactyly, is a fixed flexion deformity of a digit.

This condition is normally discovered at birth. If other symptoms are present, a specific syndrome may be indicated. Diagnosis of a specific syndrome is based on family history, medical history, and a physical exam. Webbed toes are also known as "twin toes," "duck toes," "turkey toes" and "tiger toes."

Severity can vary. Most cases involve the second and third toes but any number of toes can be involved. In some cases the toes are joined part way while in some the webbing can extend right up to the nails. In some cases the entire toes, including the nails and bones, can be fused.

Due to a developmental arrest there is an abnormal alignment of the joint surfaces at either interphalangeal joint causing angulation in the plane of the palm. The finger may be slightly bent or have a very prominent bend.

The exact cause of the condition is unknown. In some cases, close family members may share this condition. In other cases, no other related persons have this condition. The scientific name for the condition is syndactyly, although this term covers both webbed fingers and webbed toes. Syndactyly occurs when apoptosis or programmed cell death during gestation is absent or incomplete. Webbed toes occur most commonly in the following circumstances:

- Syndactyly or Familial Syndactyly

- Down syndrome

It is also associated with a number of rare conditions, notably:

- Aarskog–Scott syndrome

- Acrocallosal syndrome

- Apert's syndrome

- Bardet-Biedl syndrome

- Carpenter syndrome

- Cornelia de Lange syndrome

- Edwards syndrome

- Jackson–Weiss syndrome

- Fetal hydantoin syndrome

- Miller syndrome

- Pfeiffer syndrome

- Smith-Lemli-Opitz syndrome

- Timothy syndrome

- Ectodermal Dysplasia

- Klippel-Feil Syndrome

Congenital causes include: Aarskog syndrome, Albright's hereditary osteodystrophy, and Apert syndrome. Can be caused by a trauma, although the exact mechanism is not known.

Brachymetatarsia or hypoplastic metatarsal is a condition in which there is one or more abnormally short or overlapping toes metatarsals. This condition may result due to a congenital defect or it may be an acquired condition. It most frequently involves the fourth metatarsal. If it involves the first metatarsal, the condition is known as Morton's syndrome. Treatment is via a number of differing surgical procedures.

The CDC reviewed nine syndromes that have overlapping features with FAS; however, none of these syndromes include all three FAS facial features, and none are the result of prenatal alcohol exposure:

- Aarskog syndrome

- Williams syndrome

- Noonan syndrome

- Brachman-DeLange syndrome

- Toluene syndrome

- Fetal hydantoin syndrome

- Fetal valproate syndrome

- Maternal PKU fetal effects

When structural impairments are not observable or do not exist, neurological impairments are assessed. In the context of FASD, neurological impairments are caused by prenatal alcohol exposure which causes general neurological damage to the central nervous system (CNS), the peripheral nervous system, or the autonomic nervous system. A determination of a neurological problem must be made by a trained physician, and must not be due to a postnatal insult, such as a high fever, concussion, traumatic brain injury, etc.

All four diagnostic systems show virtual agreement on their criteria for CNS damage at the neurological level, and evidence of a CNS neurological impairment due to prenatal alcohol exposure will result in a diagnosis of FAS or pFAS, and functional impairments are highly likely.

Neurological problems are expressed as either hard signs, or diagnosable disorders, such as epilepsy or other seizure disorders, or soft signs. Soft signs are broader, nonspecific neurological impairments, or symptoms, such as impaired fine motor skills, neurosensory hearing loss, poor gait, clumsiness, poor eye-hand coordination. Many soft signs have norm-referenced criteria, while others are determined through clinical judgment. "Clinical judgment" is only as good as the clinician, and soft signs should be assessed by either a pediatric neurologist, a pediatric neuropsychologist, or both.