Extramammary Paget's disease is usually seen in isolation and is associated with an underlying invasive malignancy about 12% of the time. It is associated with an underlying adnexal malignancy about 24% of the time. Paget's disease of the breast is almost always associated with an underlying invasive malignancy, i.e. breast cancer (e.g. mammary ductal carcinoma).

Paget's disease of the vulva, a rare disease, may be a primary lesion or associated with adenocarcinoma originating from local organs such as the Bartholin gland, the urethra, or the rectum and thus be secondary. Patients tend to be postmenopausal.

Paget's disease of the penis may also be primary or secondary, and is even rarer than genital Paget’s disease in women. At least one case has been misdiagnosed as Bowen's disease. Isolated Paget's disease of the penis is extremely rare.

Rare diseases are usually genetic and are therefore chronic. EURORDIS estimates that at least 80% of them have identified genetic origins. Other rare diseases are the result of infections and allergies or due to degenerative and proliferative causes.

Symptoms of some rare diseases may appear at birth or in childhood, whereas others only appear once adulthood is reached.

Research publications emphasize rare diseases that are chronic or incurable, although many short-term medical conditions are also rare diseases.

An extremely rare disease of which only a few isolated cases are known.

Excellent for single-focus disease. With multi-focal disease 60% have a chronic course, 30% achieve remission and mortality is up to 10%.

Galli–Galli disease is a rare inherited condition that has close resemblance clinically to Dowling-Degos' disease, but is histologically distinct, characterized by skin lesions that are 1- to 2-mm slightly keratotic red to dark brown papules which are focally confluent in a reticulate pattern. The disease is also characterized by slowly progressive and disfiguring reticulate hyperpigmentation of the flexures, clinically and histopathologically diagnostic for Dowling-Degos disease but also associated with suprabasal, nondyskeratotic acantholysis.

Ichthyosis hystrix is a group of rare skin disorders in the ichthyosis family of skin disorders characterized by massive hyperkeratosis with an appearance like spiny scales. This term is also used to refer to a type of epidermal nevi with extensive bilateral distribution.

LCH usually affects children between 1 and 15 years old, with a peak incidence between 5 and 10 years of age. Among children under the age of 10, yearly incidence is thought to be 1 in 200,000; and in adults even rarer, in about 1 in 560,000. It has been reported in elderly but is vanishingly rare. It is most prevalent in Caucasians, and affects males twice as often as females. In other populations too the prevalence in males is slightly more than in females.

LCH is usually a sporadic and non-hereditary condition but familial clustering has been noted in limited number of cases. Hashimoto-Pritzker disease is a congenital self-healing variant of Hand-Schüller-Christian disease.

Office of Rare Diseases listed Lyngstadaas syndrome as a "rare disease". This means that Lyngstadaas syndrome, or a subtype of Lyngstadaas syndrome, affects less than 200,000 people in the US population.

Orphanet, a consortium of European partners, currently defines a condition rare when if affects 1 person per 2,000. They list Lyngstadaas syndrome as a "rare disease".

Lyngstadaas Syndrome, also known as severe dental aberrations in familial steroid dehydrogenase deficiency , is a rare autosomal recessive liver disease involving an enzyme (steroid dehydrogenase) deficiency and dental anomalies. The disease is named after the Norwegian professor Ståle Petter Lyngstadaas.

Erdheim–Chester disease is associated with high mortality rates. In 2005, the survival rate was below 50% at three years from diagnosis. More recent reports of patients treated with Interferon therapy describe an overall 5-year survival of 68%. Long term survival is currently even more promising, although this impression is not reflected in the recent literature.

Microcephalic osteodysplastic primordial dwarfism type II (MOPD II) is listed as a "rare disease" by the Office of Rare Diseases (ORD) of the National Institutes of Health (NIH). This means that MOPD, or a subtype of MOPD, affects less than 200,000 people in the US population and a form of dwarfism associated with brain and skeletal abnormalities.

It was characterized in 1982.

It is associated with "PCNT".

Surgeon Hutan Ashrafian from Imperial College London has analysed the Great Sphinx to identify that it may have represented an individual suffering from prognathism which may have been a reflection of a disease suffered by the sculpture’s human inspiration. Furthermore as the Sphinx represented a lion, the same person may have suffered from leontiasis ossea.

Prevalence (number of people living with a disease at a given moment), rather than incidence (number of new diagnoses in a given year), is used to describe the impact of rare diseases. The Global Genes Project estimates some 300 million people worldwide are affected by a rare disease.

The European Organization for Rare Diseases (EURORDIS) estimates that as many as 5,000 to 7,000 distinct rare diseases exist, and as much as 6% to 8% of the population of the European Union is affected by one. Only about 400 rare diseases have therapies and about 80% have a genetic component according to Rare Genomics Institute.

Rare diseases can vary in prevalence between populations, so a disease that is rare in some populations may be common in others. This is especially true of genetic diseases and infectious diseases. An example is cystic fibrosis, a genetic disease: it is rare in most parts of Asia but relatively common in Europe and in populations of European descent. In smaller communities, the founder effect can result in a disease that is very rare worldwide being prevalent within the smaller community. Many infectious diseases are prevalent in a given geographic area but rare everywhere else. Other diseases, such as many rare forms of cancer, have no apparent pattern of distribution but are simply rare. The classification of other conditions depends in part on the population being studied: All forms of cancer in children are generally considered rare, because so few children develop cancer, but the same cancer in adults may be more common.

About 40 rare diseases have a far higher prevalence in Finland; these are known collectively as Finnish heritage disease.

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.

The frequency is unknown, but the disease is considered to be very rare.

Leontiasis ossea, also known as leontiasis, lion face or Lion Face Syndrome, is a rare medical condition, characterized by an overgrowth of the facial and cranial bones. It is not a disease in itself, but a symptom of other diseases, including Paget's disease, fibrous dysplasia, hyperparathyroidism and renal osteodystrophy.

The common form is that in which one or other maxilla is affected, its size progressively increasing, and thus encroaching on the cavities of the orbit, the mouth, the nose and its accessory sinuses. Exophthalmos gradually develops, going on later to a complete loss of sight due to compression of the optic nerve by the overgrowth of bone. There may also be interference with the nasal respiration and with the taking of food. In the somewhat less common form of this rare disease the overgrowth of bone affects all the cranial bones as well as those of the face, the senses being lost one by one and death finally resulting from cerebral pressure. There is no treatment other than exposing the overgrown bone, and chipping away pieces, or excising entirely where possible.

The course of HPS has been mild in rare instances of the disorder, however, the general prognosis is still considered to be poor.

The disease can cause dysfunctions of the lungs, intestine, kidneys, and heart. The major complication of most forms of the disorder is pulmonary fibrosis, which typically exhibits in patients ages 40–50 years. This is a fatal complication seen in many forms of HPS, and is the usual cause of death from the disorder. HPS patients who develop pulmonary fibrosis typically have type 1 or type 4.

Lichen ruber moniliformis is a rare skin disease named for Fred Wise and Charles R. Rein.

It is one of several diseases also known as Kaposi's disease, based on its characterization in 1886 by Moritz Kaposi.

It is thought to be a rare variety of lichen planus.It is also known as "Morbus moniliformis lichenoides".

To date, the specific cause of Gorham's disease remains unknown.

Bone mass and strength are obtained and maintained through a process of bone destruction and replacement that occurs at the cellular level throughout a person's life. Cells called osteoclasts secrete enzymes that dissolve old bone, allowing another type of cells called osteoblasts to form new bone. Except in growing bone, the rate of breakdown equals the rate of building, thereby maintaining bone mass. In Gorham's disease that process is disrupted.

Gorham and Stout found that vascular anomalies always occupied space that normally would be filled with new bone and speculated that the presence of angiomatosis may lead to chemical changes in the bone. Gorham and others speculated that such a change in the bone chemistry might cause an imbalance in the rate of osteoclast activity to osteoblast activity such that more bone is dissolved than is replaced. Beginning in the 1990s there were reports of elevated levels of a protein called interleukin-6 (IL-6) being detected in patients with the disease, leading some to suggest that increased levels of IL-6 and vascular endothelial growth factor (VEGF) may contribute to the chemical changes Gorham and others believed were the cause of this type of osteolysis.

In 1999 Möller and colleagues concluded, "The Gorham-Stout syndrome may be, essentially, a monocentric bone disease with a focally increased bone resorption due to an increased number of paracrine – or autocrine – stimulated hyperactive osteoclasts. The resorbed bone is replaced by a markedly vascularized fibrous tissue. The apparent contradiction concerning the presence or absence or the number of osteoclasts, may be explained by the different phases of the syndrome." They further stated that their histopathological study provided good evidence that osteolytic changes seen in Gorham's disease are the result of hyperactive osteoclastic bone. However, others have concluded that lymphangiomatosis and Gorham's disease should be considered as a spectrum of disease rather than separate diseases.

While there is consensus that Gorham's is caused by deranged osteoclastic activity, there is not yet conclusive evidence as to what causes this deranged behavior to begin.

HPS is one of the rare lung diseases currently being studied by The Rare Lung Diseases Consortium (RLDC). The RLDC is part of the Rare Diseases Clinical Research Network (RDCRN), an initiative of the Office of Rare Diseases Research (ORDR), of the National Center for Advancing Translational Sciences (NCATS). The RLDC is dedicated to developing new diagnostics and therapeutics for patients with rare lung diseases, through collaboration between the NIH, patient organizations and clinical investigators.

Erdheim–Chester disease (also known as Erdheim–Chester syndrome or polyostotic sclerosing histiocytosis) is a rare disease characterized by the abnormal multiplication of a specific type of white blood cells called histiocytes, or tissue macrophages (technically, this disease is termed a non-Langerhans-cell histiocytosis). Onset typically is in middle age. The disease involves an infiltration of lipid-laden macrophages, multinucleated giant cells, an inflammatory infiltrate of lymphocytes and histiocytes in the bone marrow, and a generalized sclerosis of the long bones.

Ho–Kaufman–Mcalister syndrome, also known as the Chen-Kung Ho–Kaufman–Mcalister syndrome, is a rare congenital malformation syndrome where infants are born with a cleft palate, micrognathia, Wormian bones, congenital heart disease, dislocated hips, bowed fibulae, preaxial polydactyly of the feet, abnormal skin patterns, and most prominently, missing tibia. The etiology is unknown. Ho–Kaufman–Mcalister syndrome is named after Chen-Kung Ho, R.L. Kaufman, and W.H. Mcalister who first described the syndrome in 1975 at Washington University in St. Louis. It is considered a rare disease by the Office of Rare Diseases (ORD) of the National Institutes of Health (NIH).

Barakat syndrome, is a rare disease characterized by hypoparathyroidism, sensorineural deafness and renal disease, and hence also known as HDR syndrome. It was first described by Amin J. Barakat et al. in 1977.

Zeichi-Ceide syndrome is a rare disease discovered in 2007. It is named after its discoverer, R.M. Zeichi-Ceide, who observed three siblings born of consanguineous parents with distinctive characteristics, including facial anomalies, large feet, mental deficiency, and occipital atretic cephalocele. The investigators suspected the symptoms were caused by autosomal recessive inheritance.

As a rare disease, Zeichi-Ceide syndrome is registered in the Online Mendelian Inheritance in Man and the U.S. National Institutes of Health's Genetic and Rare Diseases databases.