Café au lait spots can arise from diverse and unrelated causes:

- Having six or more café au lait spots greater than 5 mm in diameter before puberty, or greater than 15 mm in diameter after puberty, is a diagnostic feature of neurofibromatosis type I, but other features are required to diagnose NF-1.

- Familial multiple café au lait spots have been observed without NF-1 diagnosis.

- They can be caused by vitiligo in the rare McCune–Albright syndrome.

- Legius syndrome

- Tuberous sclerosis

- Fanconi anemia

- Idiopathic

- Ataxia-telangiectasia

- Basal cell nevus syndrome

- Benign congenital skin lesion

- Bloom syndrome

- Chédiak–Higashi syndrome

- Congenital naevus

- Gaucher disease

- Hunter syndrome

- Jaffe–Campanacci syndrome

- Maffucci syndrome

- Multiple mucosal neuroma syndrome

- Noonan syndrome

- Pulmonary Stenosis

- Silver–Russell syndrome

- Watson syndrome

- Wiskott–Aldrich syndrome

Halo nevi are estimated to be present in approximately 1% of the general population, and are found to be more prevalent in people with vitiligo, malignant melanoma, or Turner syndrome. All races and sexes are equally susceptible to this disease, although a familial tendency has been reported. The average age of onset is in a person's teenage years.

Usually observed at birth or shortly thereafter in 94% of patients, in other reports, patients did not develop skin lesions until 3 months or even 2 years after birth. Females are typically affected more often than males (64%).

Ultraviolet light from the sun causes premature aging of the skin and skin damage that can lead to melanoma. Some scientists hypothesize that overexposure to UV, including excessive sunlight, may play a role in the formation of acquired moles. However, more research is needed to determine the complex interaction between genetic makeup and overall exposure to ultraviolet light. Some strong indications that this is so (but falling short of proof), are:

- The relative lack of moles on the buttocks of people with dysplastic nevi.

- Freckles (spots of melanin on the skin, and distinct from moles) are known to be influenced by sunlight.

Studies have found that sunburns and too much time in the sun can increase the risk factors for melanoma. This is "in addition to" those who have dysplastic nevi being at higher risk of this cancer (the uncertainty is in regard to acquiring "benign" moles). To prevent and reduce the risk of melanoma caused by UV radiation, the American Academy of Dermatology and the National Cancer Institute recommends staying out of the sun between 10 a.m. and 4 p.m. standard time (or whenever one's shadow is shorter than one's height). The National Cancer Institute also recommends wearing long sleeves and trousers, hats with a wide brim, sunscreens, and sunglasses that have UV-deflecting lenses.

Studies have recorded an incidence of about 3–5 cases per 1,000 newborn babies.

Large and especially giant congenital nevi are at higher risk for malignancy degeneration into melanoma. Because of the premalignant potential, it is an acceptable clinical practice to remove congenital nevi electively in all patients and relieve the nevocytic overload.

The prognosis is favorable in most patients with an isolated cutaneous abnormality. In the majority of cases, both the vivid red marking and the difference in circumference of the extremities regress spontaneously during the first year of life. It is theorized that this may be due to the normal maturation process, with thickening of the epidermis and dermis. Improvements for some patients can continue for up to 10 years, while in other cases, the marbled skin may persist for the patient's lifetime.

One study reported an improvement in lesions in 46% of patients within 3 years. If CMTC persists into adulthood, it can result in complaints due to paresthesia, increased sensitivity to cold and pain, and the formation of ulcers.

Few reports included long-term follow up of CMTC into adolescence and adulthood. While about 50% of patients seem to show definite improvement in the reticular vascular pattern, the exact incidence and cause of persistent cases are unknown.

Café au lait spots are usually present at birth, permanent, and may grow in size or increase in number over time.

Cafe au lait spots are themselves benign and do not cause any illness or problems. However, they may be associated with syndromes such as Neurofibromatosis Type 1 and McCune-Albright syndrome.

The size and shape of the spots do not have any meaning or implications with regards to diagnosis of associated syndromes.

Experts, such as the American Academy of Dermatology, say that vast majority of moles are benign. Nonetheless, the U.S. National Cancer Institute estimated that 62,480 new cases of melanoma and 8,420 related deaths would appear in the United States in the year 2008.

Data on the chances of transformation from melanocytic nevi to melanoma is controversial, but it appears that about 10% of malignant melanomas have a precursor lesion, of which about 10% are melanocytic nevi. Therefore, it appears that malignant melanoma quite seldomly (1% of cases) has a melanocytic nevi as a precursor.

The decision to observe or treat a nevus may depend on a number of factors, including cosmetic concerns, irritative symptoms (e.g., pruritus), ulceration, infection, and concern for potential malignancy.

Phakomatosis pigmentovascularis is a rare neurocutanous condition where there is coexistence of a capillary malformation (port-wine stain) with various melanocytic lesions, including dermal melanocytosis (Mongolian spots), nevus spilus, and nevus of Ota.

As halo nevi are only of cosmetic significance, no treatment is required, and patients will be asymptomatic. Although halo nevi are harmless, it is important to monitor the lesion on regular basis. Watch out for any changes in appearance of existing or new halo nevi. If there is any change in appearance or is associated with pain, itch, and infection, a doctor should be consulted immediately to exclude the possibility of melanoma.

Mucinous nevus (also known as "Nevus mucinosus") is a rare cutaneous condition characterized by hamartoma that can be congenital or acquired.

Naegeli–Franceschetti–Jadassohn syndrome (NFJS), also known as chromatophore nevus of Naegeli and Naegeli syndrome, is a rare autosomal dominant form of ectodermal dysplasia, characterized by reticular skin pigmentation, diminished function of the sweat glands, the absence of teeth and hyperkeratosis of the palms and soles. One of the most striking features is the absence of fingerprint lines on the fingers.

Naegeli syndrome is similar to dermatopathia pigmentosa reticularis, both of which are caused by a specific defect in the keratin 14 protein.

Phakomatosis pigmentokeratotica is a rare neurocutanous condition characterized by the combination of an organoid sebaceous nevus and speckled lentiginous nevus. It is an unusual variant of epidermal naevus syndrome. It was first described by Happle "et al". It is often associated with neurological or skeletal anomalies such as hemiatrophy, dysaesthesia and hyperhidrosis in a segmental pattern, mild mental retardation, seizures, deafness, ptosis and strabismus.

Nevus psiloliparus is a cutaneous condition, a rare scalp anomaly characterized by a variable degree of alopecia and an excessive amount of adipose tissue.

It is the main hallmark of encephalocraniocutaneous lipomatosis (ECCL), otherwise known as Haberland syndrome.

Spitz nevi are uncommon. Their annual incidence was estimated in a coastal population of sub-tropical Queensland to be 1.4 cases per 100,000 people. For comparison, the annual incidence of melanoma in the same population, which is high by world standards is 25.4 cases per 100,000 people.

Although they are most commonly found on people in their first two decades of life, the age range for people with Spitz nevi is from 6 months to 71 years, with a mean age of 22 years and a median age of 19 years.

Nevus of Ito (also known as "Nevus fuscoceruleus acromiodeltoideus") is a skin condition with similar features to the Nevus of Ota, but occurring in a different distribution.

Nevus of Ota (also known as "congenital melanosis bulbi", "nevus fuscoceruleus ophthalmomaxillaris", "oculodermal melanocytosis", and "oculomucodermal melanocytosis") is a blue hyperpigmentation that occurs on the face. It was first reported by Dr. M.T. Ota of Japan in 1939.

Nevus of Ota is caused by the entrapment of melanocytes in the upper third of the dermis. It is found on the face unilaterally and involves the first two branches of the trigeminal nerve. The sclera is involved in two-thirds of cases (causing an increased risk of glaucoma). It should not be confused with Mongolian spot, which is a birthmark caused by entrapment of melanocytes in the dermis but is located in the lumbosacral region. Women are nearly five times more likely to be affected than men, and it is rare among Caucasian people. Nevus of Ota may not be congenital, and may appear during puberty.

These nevi represent excess growth of blood vessels, including capillaries.

- Nevus simplex (also known as a stork bite, salmon patch, or Nevus flammeus neonatorum)

Schimmelpenning syndrome appears to be sporadic rather than inherited, in almost all cases. It is thought to result from genetic mosaicism, possibly an autosomal dominant mutation arising after conception and present only in a subpopulation of cells. The earlier in embryological development such a mutation occurs, the more extensive the nevi are likely to be and the greater the likelihood of other organ system involvement.

Pigmented hairy epidermal nevus syndrome is a cutaneous condition characterized by a Becker nevus, ipsilateral hypoplasia of the breast, and skeletal defects such as scoliosis.

A unibrow is part of normal human variation, but can also stem from developmental disorders. A unibrow is a recognized feature of Cornelia De Lange syndrome, a genetic disorder whose main features include moderate to severe learning difficulties, limb abnormalities such as oligodactyly (fewer than normal fingers or toes) and phocomelia (malformed limbs), and facial abnormalities including a long philtrum (the slight depression/line between the nose and mouth).

Other medical conditions associated with a unibrow include:

- Waardenburg Syndrome;

- Patau Syndrome;

- Smith-Lemli-Opitz Syndrome;

- Sanfilippo Syndrome;

- 3p Deletion Syndrome;

- Chromosome Deletion Dillan 4p Syndrome (Wolf–Hirschhorn Syndrome);

- Gorlin Syndrome (Basal Cell Nevus Syndrome);

- Frontometaphyseal Dysplasia;

- ATRX Syndrome;

- Chromosome 9q34 Microdeletion Syndrome or Kleefstra syndrome.

Nevus comedonicus (also known as a "comedo nevus") is characterized by closely arranged, grouped, often linear, slightly elevated papules that have at their center keratinous plugs resembling comedones.

A connective tissue nevus (also known as a "collagenoma", "elastoma", and "shagreen patch") may be present at birth or appear within the first few years, is elevated, soft to firm, varying from 0.5 to several centimeters in diameter, and may be grouped, linear, or irregularly distributed.