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.

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.

Surgical excision is the standard of care. Some individuals advocate the use of hair removal laser for the treatment of congenital nevi. While this is likely safe and effective for small congenital nevus, laser removal for larger lesions might pose a liability for the laser surgeon if malignancy developed from a deep (dermal) component of the nevus that is not reached by the laser. Repigmentation after laser treatment of congenital nevi or superficial curettage supports this concern.

Many are surgically removed for aesthetics and relief of psychosocial burden, but larger ones are also excised for prevention of cancer, although the benefit is impossible to assess for any individual patient. Proliferative nodules are usually biopsied and are regularly but not systematically found to be benign. Estimates of transformation into melanoma vary from 2-42% in the literature, but are most commonly considered to be at the low end of that spectrum due to early observer bias.

The management of a nevus depends on the specific diagnosis, however, the options for treatment generally include the following modalities:

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.

First, a diagnosis must be made. If the lesion is a seborrheic keratosis, then shave excision, electrodesiccation or cryosurgery may be performed, usually leaving very little if any scarring. If the lesion is suspected to be a skin cancer, a skin biopsy must be done first, before considering removal. This is unless an excisional biopsy is warranted. If the lesion is a melanocytic nevus, one has to decide if it is medically indicated or not

If a melanocytic nevus is suspected of being a melanoma, it needs to be sampled or removed and sent for microscopic evaluation by a pathologist by a method called skin biopsy. One can do a complete excisional skin biopsy or a punch skin biopsy, depending on the size and location of the original nevus. Other reasons for removal may be cosmetic, or because a raised mole interferes with daily life (e.g. shaving). Removal can be by excisional biopsy or by shaving. A shaved site leaves a red mark on the site which returns to the patient’s usual skin color in about two weeks. However, there might still be a risk of spread of the melanoma, so the methods of Melanoma diagnosis, including excisional biopsy, are still recommended even in these instances. Additionally, moles can be removed by laser, surgery or electrocautery.

In properly trained hands, some medical lasers are used to remove flat moles level with the surface of the skin, as well as some raised moles. While laser treatment is commonly offered and may require several appointments, other dermatologists think lasers are not the best method for removing moles because the laser only cauterizes or, in certain cases, removes very superficial levels of skin. Moles tend to go deeper into the skin than non-invasive lasers can penetrate. After a laser treatment a scab is formed, which falls off about seven days later, in contrast to surgery, where the wound has to be sutured. A second concern about the laser treatment is that if the lesion is a melanoma, and was misdiagnosed as a benign mole, the procedure might delay diagnosis. If the mole is incompletely removed by the laser, and the pigmented lesion regrows, it might form a recurrent nevus.

Electrocautery is available as an alternative to laser cautery. Electrocautery is a procedure that uses a light electrical current to burn moles, skin tags, and warts off the skin. Electric currents are set to a level such that they only reach the outermost layers of the skin, thus reducing the problem of scarring. Approximately 1-3 treatments may be needed to completely remove a mole. Typically, a local anesthetic is applied to the treated skin area before beginning the mole removal procedure.

For surgery, many dermatologic and plastic surgeons first use a freezing solution, usually liquid nitrogen, on a raised mole and then shave it away with a scalpel. If the surgeon opts for the shaving method, he or she usually also cauterizes the stump. Because a circle is difficult to close with stitches, the incision is usually elliptical or eye-shaped. However, freezing should not be done to a nevus suspected to be a melanoma, as the ice crystals can cause pathological changes called "freezing artifacts" which might interfere with the diagnosis of the melanoma.

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%).

Nevus sebaceus or sebaceous nevus (the first term is its Latin name, the second term is its name in English; also known as an "organoid nevus" and "nevus sebaceus of Jadassohn") is a congenital, hairless plaque that typically occurs on the face or scalp. Such nevi are present at birth, or early childhood, affecting males and females of all races equally. The condition is named for an overgrowth of sebaceous glands in the area of the nevus.

Skin growths such as benign tumors and basal cell carcinoma can arise in sebaceous nevi, usually in adulthood. Rarely, sebaceous nevi can give rise to sebaceous carcinoma. However, the rate of such malignancies is now known to be less than had been estimated. For this reason, excision is no longer automatically recommended.

A Q-switched laser has been successfully used to treat the condition.

Blue nevus (also known as "blue neuronevus", "dermal melanocytoma", and "nevus bleu") is a type of melanocytic nevus. The blue colour is caused by the pigment being deeper in the skin than in ordinary nevi. In principle they are harmless but they can sometimes be mimicked by malignant lesions, i.e. some melanomas can look like a blue nevus.

In general, there is no treatment available for CMTC, although associated abnormalities can be treated. In the case of limb asymmetry, when no functional problems are noted, treatment is not warranted, except for an elevation device for the shorter leg.

Laser therapy has not been successful in the treatment of CMTC, possibly due to the presence of many large and deep capillaries and dilated veins. Pulsed-dye laser and long-pulsed-dye laser have not yet been evaluated in CMTC, but neither argon laser therapy nor YAG laser therapy has been helpful.

When ulcers develop secondary to the congenital disease, antibiotic treatment such as oxacillin and gentamicin administered for 10 days has been prescribed. In one study, the wound grew Escherichia coli while blood cultures were negative.

In the absence of successful treatment, hypertrophy (increased tissue mass) of the stains may cause problems later in life, such as loss of function (especially if the stain is near the eye or mouth), bleeding, and increasing disfigurement. Lesions on or near the eyelid can be associated with glaucoma. If the port-wine stain is on the face or other highly visible part of the body, its presence can also cause emotional and social problems for the affected person.

It is suggested that gene therapy might be used as a cure in the future.

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

There is no treatment, but because this is a benign condition with no serious clinical complications, prognosis is excellent.

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.

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.

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

As Becker's nevus is considered a benign lesion, treatment is generally not necessary except for cosmetic purposes. Shaving or trimming can be effective in removing unwanted hair, while electrology or laser hair removal may offer a longer-lasting solution. Different types of laser treatments may also be effective in elimination or reduction of hyperpigmentation, though the results of laser treatments for both hair and pigment reduction appear to be highly variable.

Most birthmarks are harmless and do not require treatment. Pigmented marks can resolve on their own over time in some cases. Vascular birthmarks may require reduction or removal for cosmetic reasons. Treatments include administering oral or injected steroids, dermatological lasers to reduce size and/or color, or dermatologic surgery.

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

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.

Also known as "scoop", "scallop", or "shave" excisional biopsy, or "shave excision". A trend has occurred in dermatology over the last 10 years with the advocacy of a deep shave excision of a pigmented lesion An author published the result of this method and advocated it as better than standard excision and less time consuming. The added economic benefit is that many surgeons bill the procedure as an excision, rather than a shave biopsy. This save the added time for hemostasis, instruments, and suture cost. The great disadvantage, seen years later is the numerous scallop scars, and a very difficult to deal with lesions called a "recurrent melanocytic nevus". What has happened is that many "shave" excisions does not adequately penetrate the dermis or subcutanous fat enough to include the entire melanocytic lesion. Residual melanocytes regrow into the scar. The combination of scarring, inflammation, blood vessels, and atypical pigmented streaks seen in these recurrent nevus gives the perfect dermatoscopic picture of a melanoma. When a second physicians re-examine the patient, he or she has no choice but to recommend the reexcision of the scar. If one does not have access to the original pathology report, it is impossible to tell a recurring nevus from a severely dysplastic nevus or a melanoma. As the procedure is widely practiced, it is not unusual to see a patient with dozens of scallop scars, with as many as 20% of the scars showing residual pigmentation. The second issue with the shave excision is fat herniation, iatrogenic anetoderma, and hypertrophic scarring. As the deep shave excision either completely remove the full thickness of the dermis or greatly diminishing the dermal thickness, subcutanous fat can herniate outward or pucker the skin out in an unattractive way. In areas prone to friction, this can result in pain, itching, or hypertrophic scarring.

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.

Medical knowledge and documentation of this disorder is poor, likely due to a combination of factors including recent discovery, low prevalence, and the more or less aesthetic nature of the effects of the skin disorder. Thus the pathophysiology of Becker's nevus remains unclear. While it is generally considered an acquired rather than congenital disorder, there exists at least one case report documenting what researchers claim is a congenital Becker's nevus with genetic association: a 16-month-old boy with a hyperpigmented lesion on his right shoulder whose father has a similar lesion on his right shoulder.

The most extensive study to date, a 1981 survey of nearly 20,000 French males aged 17 to 26, served to disprove many commonly held beliefs about the disorder. In the French study, 100 subjects were found to have Becker's nevi, revealing a prevalence of 0.52%. Nevi appeared in one half the subjects before the age of 10, and between ages 10 and 20 in the rest. In one quarter of cases sun exposure seems to have played a role, a number apparently lower than that expected by researchers. Also surprising to researchers was the low incidence (32%) of Becker's nevi above the nipples, for it had generally been believed that the upper chest and shoulder area was the predominant site of occurrence. Pigmentation was light brown in 75% of cases (note: subjects were Caucasian), and average size of the nevus was 125 cm² (19 in²).

An Apocrine nevus is an extremely rare cutaneous condition that is composed of hyperplastic mature apocrine glands.