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

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%).

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.

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.

NBCCS has an incidence of 1 in 50,000 to 150,000 with higher incidence in Australia. One aspect of NBCCS is that basal-cell carcinomas will occur on areas of the body which are not generally exposed to sunlight, such as the palms and soles of the feet and lesions may develop at the base of palmar and plantar pits.

One of the prime features of NBCCS is development of multiple BCCs at an early age, often in the teen years. Each person who has this syndrome is affected to a different degree, some having many more characteristics of the condition than others.

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

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

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.

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.

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.

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.

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.

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 comedonicus syndrome is a cutaneous condition characterized by a nevus comedonicus associated with cataracts, scoliosis, and neurologic abnormalities.

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

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

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.

Nevoid melanoma is a cutaneous condition that may resemble a Spitz nevus or an acquired or congenital melanocytic nevus.

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.

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.

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.

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.

Schimmelpenning syndrome is a neurocutaneous condition characterized by one or more sebaceous nevi, usually appearing on the face or scalp, associated with anomalies of the central nervous system, ocular system, skeletal system, cardiovascular system, and genitourinary system.

Synonyms include: "Linear nevus sebaceous syndrome (LNSS)", "Schimmelpenning-Feuerstein-Mims syndrome", "Feuerstein-Mims syndrome", "sebaceous nevus syndrome", "Solomon syndrome", and "Jadassohn's nevus phakomatosis". "Nevus" is sometimes spelled "naevus" and "sebaceous" may also be spelled "sebaceus". "Epidermal nevus syndrome" is sometimes used as a synonym, but more often as a broader term referring to Schimmelpenning syndrome in addition to nevus comedonicus syndrome, CHILD syndrome, Becker's nevus syndrome, and phakomatosis pigmentokeratotica.

The classic Schimmelpenning syndrome diagnosis comprises a triad of sebaceous nevi, seizures, and mental retardation. The condition was first reported by Gustav Schimmelpenning in 1957 and independently reported by Feuerstein and Mims in 1962.

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.

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.