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.

A folliculosebaceous-apocrine hamartoma, also known as "follicular-apocrine hamartoma", is a benign proliferation of the folliculosebaceous-apocrine unit.

Folliculosebaceous cystic hamartoma abbreviated as (FSCH) is a rare cutaneous hamartoma consisting of dilated folliculosebaceous units invested in mesenchymal elements. it typically affects adults, have a predilection for the central face or scalp, with less than 1.5 cm dimension. Clinically, the lesions are asymptomatic, rubbery to firm in consistency, and usually occur on or above the neck in (> 90%) of cases, Histopathologically, FSCH shares several similar features to sebaceous trichofolliculoma, but it is usually possible to differentiate these two tumors.

Congenital causes include:

- Klippel Trenaunay Weber syndrome

- Maffucci syndrome

- macrodystrophia lipomatosa

- neurofibromatosis,

- lipoatrophic diabetes.

- Proteus syndrome, which by one theory accounts for the deformities of the Elephant Man

Syringomas can be found in association with other symptoms as part of a syndrome. Hailey-Hailey disease also known as familial benign chronic pemphigus is a blistering disease that can also include syringomas.

Several systemic syndromes have also been associated with syringoma including diabetes mellitus, down syndrome, Brooke-Spiegler, and Nicolau-Balus. Specifically, diabetes mellitus is strongly associated with clear cell syringoma consisting of nests of clear cells containing glycogen. It is thought that phosphorylase deficiency, resulting from elevated glucose levels seen in diabetes leads to an accumulation of glycogen in the skin and within the clear cells. The incidence of syringomas has been reported in up to 40 percent of people with Down syndrome and can be associated with a condition calcinosis cutis which requires prompt medical attention. Brooke-Spiegler syndrome is a rare autosomal dominant syndrome with cutaneous manifestations including syringomas and trichoepitheliomas. Nicolau-Balus is a rare autosomal dominant disorder consisting of atrophoderma vermiculata and syringomas.

There are a number of acquired causes of local gigantism. A body part can attain bigger size from causes as common as the following:

- inflammation, due to trauma or infection

- tumors like osteoid osteoma, melorheostosis, and lipofibromatous hamartoma

- Arteriovenous malformations occurring on a limb, before the closure of epiphyses in long bones

- Elephantiasis, which is quite common in south-east asia due to prevalence of filariasis.

- Still's disease

- amyloidosis

- acromegaly

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

Trichofolliculoma is a cutaneous condition characterized by a benign, highly structured tumor of the pilosebaceous unit.

A basaloid follicular hamartoma is a cutaneous condition characterized as distinctive benign adnexal tumor that has several described variants.

Because Cowden syndrome can be difficult to diagnose, the exact prevalence is unknown; however, it probably occurs in at least 1 in 200,000 people.

A 2010 review of 211 patients (21 from one center, and the remaining 190 from the external literature) studied the risks for cancer and Lhermitte-Duclos disease in Cowden syndrome patients.

The cumulative lifetime (age 70 years) risks were 89% for any cancer diagnosis (95% confidence interval (CI) = 80%,95%), breast cancer [female] 81% (CI = 66%,90%), LDD 32% (CI = 19%,49%), thyroid cancer 21% (CI = 14%,29%), endometrial cancer 19% (CI = 10%,32%) and renal cancer 15% (CI = 6%,32%). A previously unreported increased lifetime risk for colorectal cancer was identified (16%, CI = 8%,24%). Male CS patients had fewer cancers diagnosed than female patients and often had cancers not classically associated with CS.

Large congenital nevi are caused by a mutation in the body's cells that occurs early in embryonic development, usually within the first twelve weeks of pregnancy. Mutations are sometimes found in genes that code for NRAS and KRAS proteins. There is no known method of prevention.

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.

Most juvenile polyps are benign, however, malignancy can occur. The cumulative lifetime risk of colorectal cancer is 39% in patients with juvenile polyposis syndrome.

Hamartomas, while generally benign, can cause problems due to their location. For example, when located on the skin, especially on the face or neck, they can be very disfiguring. Cases have been reported of hamartomas the size of a small orange. They may obstruct practically any organ in the body, such as the colon, eye, etc. They are particularly likely to cause major health issues when located in the hypothalamus, kidneys, lips, or spleen. They can be removed surgically if necessary, and are not likely to recur. Prognosis will depend upon the location and size of the lesion, as well as the overall health of the patient.

Syringomas are harmless eccrine sweat duct tumors, typically found clustered on eyelids, although they may also be found in the armpits, abdomen, chest, neck, scalp or groin area including genitals in a symmetric pattern. They are skin-colored or yellowish firm, rounded bumps, 1–3 mm in diameter, and may be confused with xanthoma, milia, hidrocystoma, trichoepithelioma, and xanthelasma. They are more common in women and are most commonly found in middle-aged Asian women. While they can present at any time in life, they typically present during adolescence. They are usually not associated with any other symptoms although can sometimes cause itchiness or irritation.

Choristomas, forms of heterotopia, are closely related benign tumors, found in abnormal locations.

It is different from hamartoma. The two can be differentiated as follows: a hamartoma is disorganized overgrowth of tissues in their normal location, (eg, Peutz-Jeghers polyps) while a choristoma is normal tissue growth in an abnormal location (e.g., gastric tissue located in distal ileum in Meckel diverticulum).

Hamartomas result from an abnormal formation of normal tissue, although the underlying reasons for the abnormality are not fully understood. They grow along with, and at the same rate as, the organ from whose tissue they are made, and, unlike cancerous tumors, only rarely invade or compress surrounding structures significantly.

Fibrous hamartoma of infancy is a rapidly growing, painless, ill-defined subcutaneous or intradermal nodule that is generally solitary and less than 5 cm in size, though, rarely, multiple lesions occur synchronously.

By 1999, there were 12 reported cases.

The majority of patients are less than 2 years old, with 25% of cases being congenital. Possible locations include the trunk and limbs; usually the upper arm or shoulder. Local excision is the treatment of choice, but it may recur locally.

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.

Hair follicle nevus (also known as a "Vellus hamartoma") is a cutaneous condition that presents as a small papule from which fine hairs protrude evenly from the surface.

Eccrine angiomatous hamartoma usually appear as a solitary nodular lesion on the acral areas of the extremities, particularly the palms and soles.

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).

Congenital smooth muscle hamartoma is typically a skin colored or lightly pigmented patch or plaque with hypertrichosis.

A 1991 report documented the cases of nine patients with both Becker's nevus and malignant melanoma. Of the nine melanomas, five were in the same body area as the Becker's nevus, with only one occurring within the nevus itself. As this was apparently the first documented co-occurrence of the two diseases, there is so far no evidence of higher malignancy rates in Becker's nevi versus normal skin. Nonetheless, as with any abnormal skin growth, the nevus should be monitored regularly and any sudden changes in appearance brought to the attention of one's doctor.

Lhermitte–Duclos disease is a rare entity; approximately 222 cases of LDD have been reported in medical literature. Symptoms of the disease most commonly manifest in the third and fourth decades of life, although it may onset at any age. Men and women are equally affected, and there is not any apparent geographical pattern.