Differential diagnosis of this condition includes the Birt-Hogg-Dubé syndrome and tuberous sclerosis. As the skin lesions are typically painful, it is also often necessary to exclude other painful tumors of the skin (including blue rubber bleb nevus, leiomyoma, eccrine spiradenoma, neuroma, dermatofibroma, angiolipoma, neurilemmoma, endometrioma, glomus tumor and granular cell tumor; the mnemonic "BLEND-AN-EGG" may be helpful). Other skin lesions that may need to be considered include cylindroma, lipoma, poroma and trichoepithelioma; these tend to be painless and have other useful distinguishing features.

The skin lesions may be difficult to diagnose clinically but a punch biopsy will usually reveal a Grenz zone separating the tumour from the overlying skin. Histological examination shows dense dermal nodules composed of elongated cells with abundant eosinophilic cytoplasm arranged in fascicles (spindle cells). The nuclei are uniform, blunt-ended and cigar-shaped with only occasional mitoses. Special stains that may be of use in the diagnosis include Masson's trichrome, Van Gieson's stain and phosphotungstic acid–haematoxylin.

The renal cell carcinomas have prominent eosinophilic nucleoli surrounded by a clear halo.

Surgical excision is the preferred method of treatment for benign glomus tumors.

Desmoplastic trichoepithelioma is benign tumor and can be managed safely with surgical removal, electrodesiccation and curettage.

Syringomas can often be diagnosed clinically based on presentation, distribution patterns over the body, lack of associated symptoms and family history. A definitive diagnosis requires a skin biopsy to allow the tissue to be examined under a microscope. Histologically, syringomas have a characteristic comma ("tadpole") shaped tail of dilated, cystic eccrine ducts.

Verruciform xanthoma is uncommon, with a female:male ratio of 1:1.1

Osteochondromas are often asymptomatic and may not cause any kind of discomfort. They are often found accidentally when an X-ray is done for an unrelated reason.

- X-rays are the first tests performed that characterize a lesion. They show a clear picture of dense structures of bones, and will also indicate bone growth pertaining to osteochondroma.

- Computed Tomography (CT) scan can identify the bony lesion in great details and show the presence of calcification. These tests also provide great details, especially in soft tissues with the aide of cross-sectional images.

- Magnetic Resonance Imaging (MRI) is the most accurate method for detecting bone masses in symptomatic cases to depict precise morphology of a tumor. It is used to verify if the palpable mass is continuous with the cortex of the affected bone and to differentiate an osteochondroma from other lesions on the surface of the bone. MRI can also be used to look for cartilage on the surface of tumor and can depict any vascular complications caused by the tumor. An MRI can identify tumors of the spinal column and is often used to diagnose low grade osteosarcoma.

- Ultrasound is done if aneurysms or pseudoaneurysms and venous or arterial thrombosis is suspected. Ultrasound is an accurate method for examining the cartilaginous cap of the osteochondroma. It is also a way of pinpointing bursitis. However, it cannot be used to predict if the growth of tumor is inward in regards to the cap.

- Angiography is used to detect vascular lesions caused by osteochondroma due to ossified cartilaginous cap. It is also used to characterize malignant transformation lesions through neovascularity.

- Clinical testing such as sequence analysis can be done of the entire coding regions of both "EXT1" and "EXT2" to detect mutations.

- A biopsy of the tissue sample of the tumor can also be taken to check for cancer.

Tests for osteochondroma can also identify diseases such as secondary peripheral chondrosarcoma and Multiple osteochondromatosis. In large, secondary chondrosarcoma arises at the site of osteochondroma due to increased thickness of the cartilage cap indicating potential malignant transformation. The symptoms of multiple osteochondromatosis are similar to solitary osteochondroma, but they are often more severe. Painless bumps can arise at the site of tumor and pain and other discomforts can also take place if pressure is put on the soft tissues, nerves, or blood vessels. Dysplasia Epiphysealis Hemimelica (DEH) or Trevor's disease and metachondromatosis (MC) are considered differential diagnosis of both solitary and hereditary osteochondromas. DEH is described as a type of over growth at one or more epiphyses. Similar to osteochondroma, DEH is diagnosed prior to 15 years of age and the growth of lesions end at puberty, when the growth plates close. Metachondromatosis is a rare disorder that exhibit symptoms of both multiple osteochondromas and enchondromas in children and is also inherited in autosomal dominant mode.

Differential diagnosis includes seborrheic keratosis, verruca simplex, condyloma acuminatum, granular cell myoblastoma, vulvar intraepithelial neoplasia, bowenoid papulosis, erythroplasia of Queyrat, and verrucous carcinoma

Intraductal papillomas of the breast are benign lesions with an incidence of approximately 2-3% in humans.

Two types of intraductal papillomas are generally distinguished. The central type develops near the nipple. They are usually solitary and often arise in the period nearing menopause. On the other hand, the peripheral type are often multiple papillomas arising at the peripheral breasts, and are usually found in younger women. The peripheral type are associated with a higher risk of malignancy.

They are the most common cause of bloody nipple discharge in women age 20-40 and generally do not show up on mammography due to their small size. They may be detectable on ultrasound. A galactogram is the most definitive test but is somewhat invasive.

The masses are often too small to be palpated or felt. A galactogram is therefore necessary to rule out the lesion.

Excision is sometimes performed. Microdochectomy/microdochotomy (removal of a breast duct) is the treatment of choice.

A desmoplastic trichoepithelioma is a cutaneous condition characterized by a solitary, firm skin lesion on the face.

The primary method for treatment is surgical, not medical. Radiation and chemotherapy are not needed for benign lesions and are not effective for malignant lesions.

Benign granular cell tumors have a recurrence rate of 2% to 8% when resection margins are deemed clear of tumor infiltration. When the resection margins of a benign granular cell tumor are positive for tumor infiltration the recurrence rate is increased to 20%. Malignant lesions are aggressive and difficult to eradicate with surgery and have a recurrence rate of 32%.

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

The most common adverse effect is pain, which is usually associated with solitary lesions. Multiple tumors are less likely to be painful.

In one report, a patient with more than 400 glomus tumors had thrombocytopenia as a result of platelet sequestration (i.e. Kasabach-Merritt syndrome).

Malignant glomus tumors, or glomangiosarcomas, are extremely rare and usually represent a locally infiltrative malignancy. However, metastases do occur and are usually fatal.

People with juvenile polyps may require yearly upper and lower endoscopies with polyp excision and cytology. Their siblings may also need to be screened regularly. Malignant transformation of polyps requires surgical colectomy.

Spiradenoma, also spiroma or eccrine spiradenoma, is a cutaneous condition that is typically characterized, clinically, as a solitary, deep-seated dermal nodule of approximately one centimeter, occurring on the ventral surface of the body. Spiradenoma lesions are benign sudoriferous tumors, and have also been described as cystic epitheliomas of the sweat glands.

The histological origin is controversial.

Dermatofibromas are hard solitary slow-growing papules (rounded bumps) that may appear in a variety of colours, usually brownish to tan; they are often elevated or pedunculated. A dermatofibroma is associated with the dimple sign; by applying lateral pressure, there is a central depression of the dermatofibroma. Although typical dermatofibromas cause little or no discomfort, itching and tenderness can occur. Dermatofibromas can be found anywhere on the body, but most often they are found on the legs and arms. They occur most often in women; the male to female ratio is about 1:4. The age group in which they most commonly occur is 20 to 45 years.

Some physicians and researchers believe dermatofibromas form as a reaction to previous injuries such as insect bites or thorn pricks. They are composed of disordered collagen laid down by fibroblasts. Dermatofibromas are classed as benign skin lesions, meaning they are completely harmless, though they may be confused with a variety of subcutaneous tumours. Deep penetrating dermatofibromas may be difficult to distinguish, even histologically, from rare malignant fibrohistocytic tumours like dermatofibrosarcoma protuberans.

Dermatofibromas typically have a positive "buttonhole sign", or central dimpling in the center.

Trichoepithelioma is a neoplasm of the adnexa of the skin. Its appearance is similar to basal cell carcinoma.

One form has been mapped to chromosome 9p21.

A giant solitary trichoepithelioma is a cutaneous condition characterized by a skin lesion that may be up to several centimeters in diameter.

Benign fibrous histiocytomas (also known as dermal dendrocytoma, dermatofibroma, fibrous dermatofibroma, fibrous histiocytoma, fibroma simplex, nodular subepidermal fibrosis, and sclerosing hemangioma) are benign skin growths.

The goal of treatment is to improve the appearance of lesions since they are otherwise not serious and typically do not cause symptoms. Many treatment methods have been attempted however, complete removal is uncommon. No single treatment method has been shown to consistently work. Both medical and surgical treatments have been studied, each with variable success. Common destructive treatment methods include carbon dioxide lasers, dermabrasion, surgical excision, electrocoagulation and chemical peels. Many of these methods are very time consuming and require multiple treatment sessions.Carbon dioxide lasers are the most commonly practiced method; however, can cause thermal damage leading to scarring in the area. Medical therapies include topical atropine, topical retinoids and oral tranilast.

The most common adverse side effects include redness, skin discoloration and pain. Other side effects include blistering and scarring.

Generalized trichoepitheliomas are characterized histologically by replacement of the hair follicles by trichoepithelioma-like epithelial proliferations associated with hyperplastic sebaceous glands.

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

Isthmicoma (also known as "Infundibuloma," and "Tumor of the follicular infundibulum") are a cutaneous condition characterized by flat, keratotic papules of the head and neck, skin lesions that are usually solitary.

A solitary trichoepithelioma is a cutaneous condition characterized by a firm dermal papules or nodules most commonly occurring on the face.

Leiomyoma is the most common benign mesenchymal tumor of esophagus and second most common benign tumor of the small bowel (with gastrointestinal stromal tumor as most common). Although leiomyoma is the most common benign esophageal tumor, malignant carcinoma is still 50 times more likely. Approximately 50% of cases are found in the jejunum, followed by the ileum in 31% of cases. Almost one half of all lesions are less than 5 centimeters.