Usually encephaloceles are noticeable deformities and are diagnosed immediately after birth, but a small encephalocele in the nasal or forehead region can go undetected. Various physical and mental developmental delays can indicate the presence of encephaloceles.

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

Encephaloceles are often accompanied by craniofacial abnormalities or other brain malformations. Symptoms may include neurologic problems, hydrocephalus (cerebrospinal fluid accumulated in the brain), spastic quadriplegia (paralysis of the limbs), microcephaly (an abnormally small head), ataxia (uncoordinated muscle movement), developmental delay, vision problems, mental and growth retardation, and seizures.

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'.

The affected infant tends to be short, with a disproportionately large head. The fetal head of Infants born with iniencephaly are hyperextended while the foramen magnum is enlarged and opens through the widened pedicles. The defective neural arches directly into the upper cervical reach of the spinal canal, causing the formation of a common cavity between most of the spinal cord and the brain. The skin of the anterior chest is connected directly to the face, bypassing the formation of a neck, while the scalp is directly connected to the skin of the back. Because of this, those born with this anomaly either have a highly shortened neck or no neck at all. This causes extreme retroflexion, or backward bending, of the head in a "star-gazing" fashion. The spine is severely distorted as well along with significant shortening due to marked lordosis. The vertebrae, especially cervical, are fused together in abnormal shapes and their numbers are reduced. The spinal cord is almost always defective while the ventricular system is often dilated and the cortex is thinned. Sometimes, in the case of iniencephaly apertus, an encephalocele (sac-like protrusions of the brain through an opening in the cranium) forms.

Additional symptoms include:

- anencephaly (failure of major sections of the brain to form)

- encephalocele (cranial contents protrudes from the skull)

- cyclopia (the two eye cavities fuse into one)

- agnathia

- cleft palate

- arthrogryposis

- clubfeet

- holoprosencephaly

- spina bifida

- low-set ears

- pulmonary hypoplasia

- omphalocele

- gastroschisis

- cardiovascular disorders

- diaphragmatic hernias

- gastrointestinal atresia

- single umbilical artery

- renal abnormalities

- genu recurvatum

- hydramnios

Encephaloceles are characterized by protrusions of the brain through the skull that are sac-like and covered with membrane. They can be a groove down the middle of the upper part of the skull, between the forehead and nose, or the back of the skull. Encephaloceles are often obvious and diagnosed immediately. Sometimes small encephaloceles in the nasal and forehead are undetected.

Hydranencephaly is a condition in which the cerebral hemispheres are missing and instead filled with sacs of cerebrospinal fluid.

Midfacial malformations can be subdivided into two different groups. One group with hypertelorism, this includes FND. The other with hypotelorism (a decreased distance between the eyes), this includes holoprosencephaly (failure of development of the forebrain). In addition, a facial cleft can be classified using the Tessier classification. Each of the clefts is numbered from 0 to 14. The 15 different types of clefts are then subdivided into 4 groups, based on their anatomical position in the face: midline clefts, paramedian clefts, orbital clefts and lateral clefts. FND is a midline cleft, classified as Tessier 0/14.

Besides this, the additional anomalies seen in FND can be subdivided by region. None of these anomalies are specific for the syndrome of FND, but they do occur more often in patients with FND than in the population. The anomalies that may be present are:

- Nasal: mild anomalies to nostrils that are far apart and a broad nasal root, a notch or cleft of the nose and accessory nasal tags.

- Ocular: narrowed eye slits, almond shaped eyes, epicanthal folds (extra eyelid tissue), epibulbar dermoids (benign tumors of the eye), upper eyelid colombas (full thickness upper eyelid defects), microphtalmos (one or two small eyes), congenital cataract and degeneration of the eye with retinal detachment.

- Facial: telecanthus (an increased distance between the corners of the eye), a median cleft of the upper lip and/or palatum, and a V-shaped hairline.

- Others: polydactyly (an excess of fingers or toes), syndactyly (fused fingers or toes), brachydactyly (short fingers and/or toes), clinodactyly (bending of the fifth fingers towards the fourth fingers), preauricular skin tags, an absent tragus, low set ears, deafness, small frontal sinuses, mental retardation, encephalocele (protrusion of the brain), spina bifida (split spine), meningoencephalocele (protrusion of both meninges), umbilical hernia, cryptorchidism (absence of one or two testes) and possibly cardiac anomalies.

The clefts of the face that are present in FND are vertical clefts. These can differ in severity. When they are less severe, they often present with hypertelorism and normal brain development.

Mental retardation is more likely when the hypertelorism is more severe or when extracephalic anomalies occur.

Cranioschisis (Greek: "κρανιον - kranion" "skull", and "schisis - σχίσις" - "split") is a developmental birth defect involving the skull. In this disease, the cranium fails to close completely (especially at the occipital region). Thus, the brain is exposed to the amnios, and eventually degenerates, causing anencephaly.

This is a classification based on the embryological cause of FND.

There are four main signs of acalvaria: absence of the flat bones of the cranial vault, absence of the dura mater and muscles associated with it, skull abnormalities, and the absence of a skull cap. This condition can be diagnosed prior to birth using ultrasonography. Physicians often use magnetic resonance imaging to confirm the diagnosis because in utero, acalvaria is sometimes confused with anencephaly or encephalocele. A distinguishable difference is that with anencephaly, the cerebral hemispheres are missing, but with acalvaria, all parts of the cerebrum are usually present and developed, whereas parts of the calvarium are missing.

Patients come to clinical attention early in life (usually at birth or within the first few months), with a firm subcutaneous nodule at bridge of nose, or as a polypoid mass within the nasal cavity, or somewhere along the upper border of the nasal bow. If the patient presents with an intranasal mass, there may be obstruction, chronic rhinosinusitis, or nasal drainage. If there is a concurrent cerebrospinal fluid (CSF) leak, then an encephalocele is much more likely.

This lesion is separated into two types based on the anatomic site of presentation:

1. Extranasal (60%): Subcutaneous bridge of nose

2. Intranasal (30%): Superior nasal cavity

3. Mixed (10%): Subcutaneous tissues and nasal cavity (larger lesions)

Nasal dysplasia or nasoschisis is caused by a development arrest of the lateral side of the nose, resulting in a cleft in one of the nasal halves. The nasal septum and cavity can be involved, though this is rare. Nasoschisis is also characterized by hypertelorism.

Acalvaria is a rare malformation consisting of absence of the calvarial bones, dura mater and associated muscles in the presence of a normal skull base and normal facial bones. The central nervous system is usually unaffected. The presumed pathogenesis of acalvaria is faulty migration of the membranous neurocranium with normal placement of the embryonic ectoderm, resulting in absence of the calvaria but an intact layer of skin over the brain parenchyma. In other words, instead of having a skull cap protecting the brain, there is only skin covering it. The size of the area that is missing the skull cap can vary from case to case. In extreme cases, the entire top part of the cranium that is dome-shaped may be absent.

While nasal glial heterotopia (NGH) is the preferred term, synonyms have included nasal glioma. However, this term is to be discouraged, as it implies a neoplasm or tumor, which it is not. By definition, nasal glial heterotopia is a specific type of choristoma. It is not a teratoma, however, which is a neoplasm comprising all three germ cell layers (ectoderm, endoderm, mesoderm). As a congenital malformation or ectopia, it is distinctly different from the trauma or iatrogenic development of an encephalocele.

Internasal dysplasia is caused by a development arrest before the union of the both nasal halves. These clefts are characterized by a median cleft lip, a median notch of the cupid's bow or a duplication of the labial frenulum. Besides the median cleft lip, hypertelorism can be seen in these clefts. Also sometimes there can be an underdevelopment of the premaxilla.

Craniopagus twins are conjoined twins that are fused at the cranium. This condition occurs in about 10–20 babies in every million births in the United States. Among this small group, cephalic conjoining, or craniopagus twinning, represents the rarest of congenital abnormalities, accounting for 2–6% of all conjoined twins. Additionally, conjoined twins are genetically identical and always share the same sex. The union in craniopagus twins may occur on any portion of the Calvary, but does not include either the face or the foramen magnum. The thorax and abdomen are separate and each twin has its own umbilicus and umbilical cord. The union may involve the entire diameter of the head or only a small portion. This suggests that although there are many different kinds of vulnerabilities already known in the scientific community, there are an infinite number of variations that can occur. Most of these variations are based on the rotation of one twin's skull to the other and the different phenotype sub-groups of craniopagus twins are based on all these rotational conformations. Each of these factors (rotation, spot of union) affects the development of the brain, the vascular system within the brain and overall wellness of life both of the twins have outside the womb. Relatively few craniopagus twins survive the perinatal period – approximately 40% of conjoined twins are stillborn and an additional 33% die within the immediate perinatal period, usually from organ abnormalities and failure. However 25% of craniopagus twins survive and can be considered for a surgical separation and several attempts occur yearly worldwide. In the last-half century, many advances in medicine including brain imaging, neuro-anesthesia and neurosurgical techniques have proven that a successful outcome is possible following separation of total craniopagus twins.

Craniotabes is softening or thinning of the skull in infants and children, which may be normally present in newborns. It is seen mostly in the occipital and parietal bones. The bones are soft, and when pressure is applied they will collapse underneath it. When the pressure is relieved, the bones will usually snap back into place.

There are two categories of craniopagus twins:

- Partial Although partial craniopagus is less common than total, it is still a division of craniopagus twins that is worth exploring. This type of twinning is defined as having limited surface area involvement, with either intact crania or cranial defects. In other words, it is a defect of the cranial "coverings." In partial craniopagus twins, the unions are usually frontal and less commonly occipital and vertical. Angular frontal junctions occur when the two twins are joined at any part of the forehead. Occipital twins are joined at the occipital lobe in the back of the head and vertical are joined on the top of the head and usually face opposite directions. The junctional diameter is often smaller in partial forms and occasionally an incomplete layer of bone may be present between the twins. Each child maintains independent calvarial convexities except at the common area of skull junction. The dura of both children may be intact or deficient and cortical gyri may interdigitate. Additionally shared dural venous sinuses is usually absent or if it is present it is negligible. These twins usually undergo successful separation and both twins may live to lead normal lives.

- Total Total craniopagus twins are defined as sharing extensive surface area with widely connected cranial cavities. Among total craniopagus twins, there are four main categories which are then further divided into several subcategories. Frontal, the first category, are when twins are facing each other with the axis of the bodies forming an acute angle. Temporoparietal craniopagi are joined immediately above the external auditory meatus. The third division is the occipital anomaly where the twins are connected in the occipital lobe causing the twins to face away from each other. The final variant is the parietal craniopagus which occurs when twins fuse at the vertex with the axis of the twins forming an obtuse angle. This category is perhaps the most important, or most interesting because the craniums of the two twins share the most veins, lobes and circuitry and is often described as one brain shared by two individuals.

- "Type 1": both children face in the same general directional axis so that the angle between twins is less than 40 degrees. These twins show relatively symmetric superior bi-parietal or vertex compressional flattening.

- "Type 2": both children face opposite directions so that the deformity shows an axial rotation between 140-180 degrees.

- "Type 3": in this variety axial rotation is intermediate between the first two types with a rotation of being between 40 and 140.

Any condition that affects bone growth, most notably rickets (from vitamin D deficiency), marasmus, syphilis, or thalassemia, can cause craniotabes if present during a time of rapid skull growth (most especially during gestation and infancy). It can be a "normal" feature in premature infants. It is the first sign in children and infants with rickets.

Limb body wall complex (LBWC) is a rare fetal malformation of unknown origins.

Traditionally diagnosis has been based on the Van Allen et al., criteria, i.e. the presence of two out of three of the following anomalies:

1. Exencephaly or encephalocele with facial clefts

2. Thoraco and or abdominoschisis and

3. Limb defects.

LBWC occurs in approximately 0.32 in 100,000 births.

At this time, there is no known cause of Limb Body Wall Complex. However, there have been tentative links made between a diagnosis of LBWC and cocaine use. In addition, current research has shown that there may be a genetic cause for a small limited number of LBWC cases.

Limb Body Wall Complex is a lethal birth defect. There are only anecdotal stories of survivors.

Very frequent signs

- Abnormal gastrointestinal tract

- Absent pectoral muscles

- Brachydactyly (Short fingers)

- Dextrocardia

- Diaphragmatic hernia/defect

- Humerus absent/abnormal

- Liver/biliary tract anomalies

- Maternal diabetes

- Oligodactyly/missing fingers

- Radius absent/abnormal

- Rhizomelic micromelia (relatively shorter proximal segment of the limbs compared to the middle and the distal segments)

- Sparsity or abnormality of axillary hair on affected side

- Syndactyly of fingers (webbing)

- Ulna absent/abnormal

- Upper limb asymmetry

- Abnormal rib

- Simian crease on affected side

Frequent signs

- Hypoplastic/absent nipples

- Scapula anomaly

Occasional signs

- Agenesis/hypoplasia of kidneys

- Encephalocele/exencephaly

- Abnormal morphology of hypothalamic-hypophyseal axis

- Abnormal function of hypothalamic-hypophyseal axis

- Microcephaly

- Preaxial polydactyly

- Ureteric anomalies (reflux/duplex system)

- Vertebral segmentation anomaly

The symptoms of phocomelia syndrome are undeveloped limbs and absent pelvic bones; however, various abnormalities can occur to the limbs and bones. Usually the upper limbs are not fully formed and sections of the "hands and arms may be missing." Short arm bones, fused fingers, and missing thumbs will often occur. Legs and feet are also affected similarly to the arms and hands. Individuals with phocomelia will often lack thigh bones, and the hands or feet may be abnormally small or appear as stumps due to their close "attachment to the body."

According to NORD, individuals carrying phocomelia syndrome will generally show symptoms of growth retardation previous to and after birth. The syndrome can also cause severe mental deficiencies in infants. Infants born with phocomelia will normally have a petite head with "sparse hair" that may appear "silvery-blonde." Hemangioma, the abnormal buildup of blood vessels, will possibly develop around the facial area at birth and the eyes may be set widely apart, a condition known as orbital hypertelorism. The pigment of the eyes will be a bluish white. Phocomelia can also cause: an undeveloped nose with slender nostrils, disfigured ears, irregularly petite jaws [also known as micrognathia], and a cleft lip with cleft palate. According to NORD, severe symptoms of phocomelia include:

- A fissure of the skull and a projecting brain known as (encephalocele)

- An accumulation of spinal fluid under the skull also known as hydrocephalus; causing vomiting and migraines

- An abnormally shaped uterus (bicornuate)

- Inability to clot blood efficiently due to a low amount of platelets running through the blood

- Malformations in the kidney and heart

- Shortened neck

- Abnormalities in the urethra

The following is a list of symptoms that have been associated with Roberts syndrome:

- Bilateral Symmetric Tetraphocomelia- a birth defect in which the hands and feet are attached to shortened arms and legs

- Prenatal Growth Retardation

- Hypomelia (Hypoplasia)- the incomplete development of a tissue or organ; less drastic than aplasia, which is no development at all

- Oligodactyly- fewer than normal number of fingers or toes

- Thumb Aplasia- the absence of a thumb

- Syndactyly- condition in which two or more fingers (or toes) are joined together; the joining can involve the bones or just the skin between the fingers

- Clinodactyly- curving of the fifth finger (little finger) towards the fourth finger (ring finger) due to the underdevelopment of the middle bone in the fifth finger

- Elbow/Knee Flexion Contractures- an inability to fully straighten the arm or leg

- Cleft Lip- the presence of one or two vertical fissures in the upper lip; can be on one side (unilateral) or on both sides (bilateral)

- Cleft Palate- opening in the roof of the mouth

- Premaxillary Protrusion- upper part of the mouth sticks out farther than the lower part of the mouth

- Micrognathia- small chin

- Microbrachycephaly- smaller than normal head size

- Malar Hypoplasia- underdevelopment of the cheek bones

- Downslanting Palpebral Fissures- the outer corners of the eyes point downwards

- Ocular Hypertelorism- unusually wide-set eyes

- Exophthalmos- a protruding eyeball

- Corneal Clouding- clouding of the front-most part of the eye

- Hypoplastic Nasal Alae- narrowing of the nostrils that can decrease the width of the nasal base

- Beaked Nose- a nose with a prominent bridge that gives it the appearance of being curved

- Ear Malformations

- Intellectual disability

- Encephalocele (only in severe cases)- rare defect of the neural tube characterized by sac-like protrusions of the brain

Mortality is high among those severely affected by Roberts syndrome; however, mildly affected individuals may survive to adulthood