Neonatal complications (apart from congenital anomalies) are common. In a paper published in 2010, 41 of 42 individuals had some type medical problem in the first days of life, the most common being feeding difficulties. Respiratory difficulty and jaundice are also relatively frequent.

The most common gastrointestinal abnormality is chronic constipation, though gastrointestinal reflux was also common.

There are various symptoms of colpocephaly and patients can experience effects ranging from mild to severe. Some patients do not show most of the symptoms related to colpocephaly, such as psychomotor abnormalilities and agenesis of the corpus callosum. In some cases, signs appear later on in life and a significant number of children suffer only from minor disabilities.

The following list includes common symptoms of colpocephaly.

- partial or complete agenesis of the corpus callosum

- intellectual disability

- motor abnormalities

- visual defects such as, crossing of the eyes, missing visual fields, and optic nerve hypoplasia

- spasticity

- seizures

- cerebral palsy

Intracranial abnormalities include:

- Microcephaly

- Agenesis of the corpus callosum

- Meningomyelocele

- Lissencephaly

- Periventricular leukomalacia (PVL)

- Enlargement of the cisterna magna

- Cerebellar hypoplasia

The following features are observed with VACTERL association:

- V - Vertebral anomalies

- A - Anorectal malformations

- C - Cardiovascular anomalies

- T - Tracheoesophageal fistula

- E - Esophageal atresia

- R - Renal (Kidney) and/or radial anomalies

- L - Limb defects

Although it was not conclusive whether VACTERL should be defined by at least two or three component defects, it is typically defined by the presence of at least three of the above congenital malformations.

Heart abnormalities are present in 25–35% of people with distal 18q-. The majority of these defects are septal. Congenital orthopedic anomalies are also relatively common, particularly rocker-bottom feet or clubfoot. Cleft lip and palate are relatively common in people with distal 18q-. Kidney abnormalities have also been reported and include horseshoe kidney, hydronephrosis, polycystic kidney, and absent kidney. Boys with distal 18q- may have genital anomalies, the most frequent being cryptorchidism and hypospadias.

Hypotonia is a common finding. Around 10% of people with distal 18q- have seizures.

Renal (kidney) defects are seen in approximately 50 percent of patients with VACTERL association. In addition, up to 35 percent of patients with VACTERL association have a single umbilical artery (there are usually two arteries and one vein) which is often associated with additional kidney or urologic problems. Renal abnormalities in VACTERL association can be severe, with incomplete formation of one or both kidneys or urologic abnormalities such as obstruction of outflow of urine from the kidneys or severe reflux (backflow) of urine into the kidneys from the bladder. These problems can cause kidney failure early in life and may require kidney transplant. Many of these problems can be corrected surgically before any damage can occur.

Colpocephaly is characterized by disproportionately large occipital horns of the lateral ventricles (also frontal and temporal ventricles in some cases). MRI and CT scans of patients demonstrate abnormally thick gray matter with thin poorly myelinated white matter. This happens as a result of partial or complete absence of the corpus callosum. Corpus callosum is the band of white matter connecting the two cerebral hemispheres. The corpus callosum plays an extremely important role in interhemispheric communication, thus lack of or absence of these neural fibers results in a number of disabilities.

The lemon sign on CT scans of patients refers to the shape of the fetal skull when the frontal bones lose their normal convex contour and appear flattened or inwardly scalloped. This gives the skull a shape similar to that of a lemon. The sign is seen on transverse sonograms of the fetal cranium obtained at the level of the ventricles.

A special case is found in literature where lissencephaly, colpocephaly, and septal agenesis are all present together. The CT scans of the patient shows the ventricular system having a unique appearance of a crown of a king. This is referred to as the 'CROWN SIGN'.

Robinow noted the resemblance of affected patients' faces to that of a fetus, using the term "fetal facies" to describe the appearance of a small face and widely spaced eyes. Clinical features also may include a short, upturned nose, a prominent forehead, and a flat nasal bridge. The upper lip may be "tented", exposing dental crowding, "tongue tie", or gum hypertrophy.

Though the eyes do not protrude, abnormalities in the lower eyelid may give that impression. Surgery may be necessary if the eyes cannot close fully. In addition, the ears may be set low on the head or have a deformed pinna.

Patients suffer from dwarfism, short lower arms, small feet, and small hands. Fingers and toes may also be abnormally short and laterally or medially bent. The thumb may be displaced and some patients, notably in Turkey, experience ectrodactyly. All patients often suffer from vertebral segmentation abnormalities. Those with the dominant variant have, at most, a single butterfly vertebra. Those with the recessive form, however, may suffer from hemivertebrae, vertebral fusion, and rib anomalies. Some cases resemble Jarcho-Levin syndrome or spondylocostal dysostosis.

Genital defects characteristically seen in males include a micropenis with a normally developed scrotum and testes. Sometimes, testicles may be undescended, or the patient may suffer from hypospadias. Female genital defects may include a reduced size clitoris and underdeveloped labia minora. Infrequently, the labia majora may also be underdeveloped. Some research has shown that females may experience vaginal atresia or haematocolpos.

The autosomal recessive form of the disorder tends to be much more severe. Examples of differences are summarized in the following table:

Sometimes babies born with choanal atresia also have other abnormalities:

- coloboma

- heart defects

- mental retardation

- growth impairment

- others (see also CHARGE syndrome)

Also any condition that causes significant depression of the nasal bridge or midface retraction can be associated with choanal atresia. Examples include the craniosynostosis syndromes such as Crouzon syndrome, Pfeiffer syndrome, Treacher Collins and Antley-Bixler syndrome.

Other signs of Alagille syndrome include congenital heart problems varying from heart murmurs (from pulmonary artery stenosis) to significant structural abnormalities, such as Tetralogy of Fallot. pulmonary stenosis is common amongst Alagille patients and other defects ; overriding aorta; ventricular septal defect; and right ventricular hypertrophy. Untreated Tetralogy of Fallot mortality rates range from 70 percent by age 10 to 95 percent by age 40. However, complete surgical repair can significantly improve both longevity and quality of life in Alagille's patients. Patients may also present with ventricular septal defects, atrial septal defects, patent ductus arteriosus and coarctation of the aorta.

Antley–Bixler syndrome presents itself at birth or prenatally. Features of the disorder include brachycephaly (flat forehead), craniosynostosis (complete skull-joint closure) of both coronal and lambdoid sutures, facial hypoplasia (underdevelopment); bowed ulna (forearm bone) and femur (thigh bone), synostosis of the radius (forearm bone), humerus (upper arm bone), and trapezoid (hand bone); camptodactyly (fused interphalangeal joints in the fingers), thin ilial wings (outer pelvic plate), and renal malformations.

Other symptoms, such as cardiac malformations, proptotic exophthalmos (bulging eyes), arachnodactyly (spider-like fingers), as well as nasal, anal, and vaginal atresia (occlusion) have been reported.

Robinow syndrome is an extremely rare genetic disorder characterized by short-limbed dwarfism, abnormalities in the head, face, and external genitalia, as well as vertebral segmentation. The disorder was first described in 1969 by human geneticist Meinhard Robinow, along with physicians Frederic N. Silverman and Hugo D. Smith, in the "American Journal of Diseases of Children". By 2002, over 100 cases had been documented and introduced into medical literature.

Two forms of the disorder exist, dominant and recessive, of which the former is more common. Patients with the dominant version often suffer moderately from the aforementioned symptoms. Recessive cases, on the other hand, are usually more physically marked, and individuals may exhibit more skeletal abnormalities. The recessive form is particularly frequent in Turkey. However, this can likely be explained by a common ancestor, as these patients' families can be traced to a single town in Eastern Turkey. Clusters of the autosomal recessive form have also been documented in Oman and Czechoslovakia.

The syndrome is also known as Robinow-Silverman-Smith syndrome, Robinow dwarfism, fetal face, fetal face syndrome, fetal facies syndrome, acral dysostosis with facial and genital abnormalities, or mesomelic dwarfism-small genitalia syndrome. The recessive form was previously known as Covesdem syndrome.

Classification systems for malformations of the cerebellum are varied and are constantly being revised as greater understanding of the underlying genetics and embryology of the disorders is uncovered. A classification proposed by Patel S in 2002 divides cerebellar malformations in two broad groups; those with cerebellar hypoplasia and; those with cerebellar dysplasia.

- I. Cerebellar hypoplasia

- A. Focal hypoplasia

- 1. Isolated vermis

- 2. One hemisphere hypoplasia

- B. Generalized hypoplasia

- 1. With enlarged fourth ventricle (“cyst,”), Dandy-Walker continuum

- 2. Normal fourth ventricle (no “cyst”)

- a. With normal pons

- b. With small pons i. Normal foliation

- a) Pontocerebellar hypoplasias of Barth, types I and II

- b) Cerebellar hypoplasias, not otherwise specified

Signs and symptoms arising from liver damage in Alagille syndrome may include a yellowish tinge in the skin and the whites of the eyes (jaundice), itching (pruritus), pale stools (acholia), an enlarged liver (hepatomegaly), an enlarged spleen (splenomegaly) and deposits of cholesterol in the skin (xanthomas). A liver biopsy may indicate too few bile ducts (bile duct paucity) or, in some cases, the complete absence of bile ducts (biliary atresia). Bile duct paucity results in the reduced absorption of fat and vitamins (A, D, E and K), which may lead to rickets or a failure to thrive in children. Around 15% of patients will experience liver cirrhosis in the course of their disease. Hepatocellular cancer has been reported in a number of cases.

It can be unilateral or bilateral.

- Sometimes, a unilateral choanal atresia is not detected until much later in life because the baby manages to get along with only one nostril available for breathing.

- Bilateral choanal atresia is a very serious life-threatening condition because the baby will then be unable to breathe directly after birth as babies are obligate nasal breathers (they mainly use their noses to breathe). In some cases, this may present as cyanosis while the baby is feeding, because the oral air passages are blocked by the tongue, further restricting the airway. The cyanosis may improve when the baby cries, as the oral airway is used at this time. These babies may require airway resuscitation soon after birth.

CHARGE syndrome (formerly known as CHARGE association), is a rare syndrome caused by a genetic disorder. First described in 1979, the acronym "CHARGE" came into use for newborn children with the congenital features of coloboma of the eye, heart defects, atresia of the nasal choanae, retardation of growth and/or development, genital and/or urinary abnormalities, and ear abnormalities and deafness. These features are no longer used in making a diagnosis of CHARGE syndrome, but the name remains. About two thirds of cases are due to a CHD7 mutation. CHARGE syndrome occurs only in 0.1–1.2 per 10,000 live births; as of 2009 it was the leading cause of congenital deafblindness in the US.

The diagnosis is based on the following clinical findings:

- microcephaly

- clinodactyly and shortness of index and little fingers

- syndactyly of 2nd & 3rd and 4th & 5th toe

- short palpebral fissures

- esophageal and/or duodenal atresia

Ring 18 causes a wide range of medical and developmental concerns. As discussed above, people with ring 18 can have features of both distal 18q- and 18p-. The features of distal 18q- and 18p- vary greatly because of the variability of the deletion size and breakpoint locations between people. Because ring 18 can involve unique deletions of both the p and q arms of the chromosome there is twice as much reason for the variability between individuals. This variation is also partly attributable to the incidence of mosaicism, which is relatively common in people with ring 18.

- Holoprosencephaly has been reported in some people with ring 18. This is due to the deletion of the TGIF gene on the short arm of chromosome 18 in some people with ring 18.Approximately 30-40% of people with ring 18 have a congenital heart anomaly. Septal defects are the most common type of defect reported in this population.

- Hypotonia is frequently seen in the ring 18 population. Seizures, though uncommon, have been reported in people with ring 18.

- In some children without “classic” holoprosencephaly, microforms of holoprosencephaly may be noted on MRI, including missing olfactory tracts and bulbs and absent or hypoplastic corpus callosum.

- Strabismus as well as nystagmus have both been reported in infants and children with ring 18.

- Hearing loss has been reported and may be related to ear canal atresia or stenosis.

- Umbilical and inguinal hernias have been reported in a small number of people with ring 18.

- Unilateral renal hypoplasia and aplasia have both been reported in individuals with ring 18. Hydronephrosis as well as pyelonephritis have also been reported in a few individuals. Cryptorchidism, hypospadias, and micropenis have been seen in males with ring 18, while females have been reported with hypoplastic labia.

- Foot abnormalities are common within the ring 18 population. Scoliosis as well as pectus excavatum have also been frequently reported.

- Several people with ring 18 have growth hormone deficiency. Hypothyroidism has also been reported in a minority of people.

- Cognitive ability varies; according to a literature review, the degree of impairment may fall anywhere between the mild and severe ends of the spectrum.

- Facial features of ring 18 include low-set, dysplastic ears, epicanthic folds, and hypertelorism. Micrognathia has also been reported.

There are frequent associated congenital anomalies all related to deviations in the development of anatomical asymmetries in early embryonic stages. These conditions considered together are called "polysplenia syndrome".

Associated conditions include heterotaxy syndrome, intestinal malrotation, situs inversus, biliary atresia, and several cardiac malformations. Associated cardiac conditions include dextrocardia, atrial situs ambiguus, ventricular inversion, and VA concordance with left posterior aorta.

Although present, the multiple small spleens are often ineffective; this is termed functional asplenia.

Non-progressive early onset ataxia and poor motor learning are the commonest presentation.

Feingold syndrome is marked by various combinations of microcephaly, limb malformations, esophageal and duodenal atresias, and sometimes learning disability or mental retardation.

Ring 18 is a genetic condition caused by a deletion of the two tips of chromosome 18 followed by the formation of a ring-shaped chromosome. It was first reported in 1964.

Although genetic testing positively identifies nearly two thirds of children with CHARGE syndrome, diagnosis is still largely clinical. The following signs were originally identified in children with this syndrome, but are no longer used in to make the diagnosis alone.

- C - Coloboma of the eye, central nervous system anomalies

- H - Heart defects

- A - Atresia of the choanae

- R - Retardation of growth and/or development

- G - Genital and/or urinary defects (Hypogonadism, undescended testicles, besides hypospadias.)

- E - Ear anomalies and/or deafness and abnormally bowl-shaped and concave ears, known as "lop ears".

Imperforate anus is associated with an increased incidence of some other specific anomalies as well, together being called the VACTERL association:

- V – Vertebral anomalies

- A – "Anal atresia"

- C – Cardiovascular anomalies

- T – Tracheoesophageal fistula

- E – Esophageal atresia

- R – Renal (kidney) and/or radial anomalies

- L – Limb defects

Other entities associated with an imperforate anus are trisomies 18 and 21, the cat-eye syndrome (partial trisomy or tetrasomy of a maternally derived number 22 chromosome), Baller-Gerold syndrome, Currarino syndrome, caudal regression syndrome, FG syndrome, Johanson-Blizzard syndrome, McKusick-Kaufman syndrome, Pallister-Hall syndrome, short rib-polydactyly syndrome type 1, Townes-Brocks syndrome, 13q deletion syndrome, urorectal septum malformation sequence, and the OEIS complex (omphalocele, exstrophy of the cloaca, imperforate anus, spinal defects).