Despite much research, the causes remain unclear but include repetitive physical trauma, ischemia (restriction of blood flow), hereditary and endocrine factors, avascular necrosis (loss of blood flow), rapid growth, deficiencies and imbalances in the ratio of calcium to phosphorus, and problems of bone formation. Although the name "osteochondritis" implies inflammation, the lack of inflammatory cells in histological examination suggests a non-inflammatory cause. It is thought that repetitive microtrauma, which leads to microfractures and sometimes an interruption of blood supply to the subchondral bone, may cause subsequent localized loss of blood supply or alteration of growth.

Trauma, rather than avascular necrosis, is thought to cause osteochondritis dissecans in juveniles. In adults, trauma is thought to be the main or perhaps the sole cause, and may be endogenous, exogenous or both. The incidence of repetitive strain injury in young athletes is on the rise and accounts for a significant number of visits to primary care; this reinforces the theory that OCD may be associated with increased participation in sports and subsequent trauma. High-impact sports such as gymnastics, soccer, basketball, lacrosse, football, tennis, squash, baseball and weight lifting may put participants at a higher risk of OCD in stressed joints (knees, ankles and elbows).

Recent case reports suggest that some people may be genetically predisposed to OCD. Families with OCD may have mutations in the aggrecan gene. Studies in horses have implicated specific genetic defects.

Heterotopic ossification of varying severity can be caused by surgery or trauma to the hips and legs. About every third patient who has total hip arthroplasty (joint replacement) or a severe fracture of the long bones of the lower leg will develop heterotopic ossification, but is uncommonly symptomatic. Between 50% and 90% of patients who developed heterotopic ossification following a previous hip arthroplasty will develop additional heterotopic ossification.

Heterotopic ossification often develops in patients with traumatic brain or spinal cord injuries, other severe neurologic disorders or severe burns, most commonly around the hips. The mechanism is unknown. This may account for the clinical impression that traumatic brain injuries cause accelerated fracture healing.

There are also rare genetic disorders causing heterotopic ossification such as fibrodysplasia ossificans progressiva (FOP), a condition that causes injured bodily tissues to be replaced by heterotopic bone. Characteristically exhibiting in the big toe at birth, it causes the formation of heterotopic bone throughout the body over the course of the sufferer's life, causing chronic pain and eventually leading to the immobilisation and fusion of most of the skeleton by abnormal growths of bone.

Another rare genetic disorder causing heterotopic ossification is progressive osseous heteroplasia (POH), is a condition characterized by cutaneous or subcutaneous ossification.

The exact cause is unknown. Mechanical factors, dietary and long term use of some antidepressants may be of significance. There is a correlation between these factors but not a cause or effect. The distinctive radiological feature of DISH is the continuous linear calcification along the antero-medial aspect of the thoracic spine. The disease is usually found in people in their 60s and above, and is extremely rare in people in their 40s and 30s. The disease can spread to any joint of the body, affecting the neck, shoulders, ribs, hips, pelvis, knees, ankles, and hands. The disease is not fatal, however some associated complications can lead to death. Complications include paralysis, dysphagia (the inability to swallow), and pulmonary infections. Although DISH manifests in a similar manner to ankylosing spondylitis, these two are totally separate diseases. Ankylosing spondylitis is a genetic disease with identifiable marks, and affects organs. DISH has no indication of a genetic link, and does not affect organs other than the lungs, which is only indirect due to the fusion of the rib cage.

Long term treatment of acne with vitamin derived retinoids, such as etretinate and acitretin, have been associated with "extraspinal" hyperostosis.

OCD is a relatively rare disorder, with an estimated incidence of 15 to 30 cases per 100,000 persons per year. Widuchowski W "et al." found OCD to be the cause of articular cartilage defects in 2% of cases in a study of 25,124 knee arthroscopies. Although rare, OCD is noted as an important cause of joint pain in active adolescents. The juvenile form of the disease occurs in children with open growth plates, usually between the ages 5 and 15 years and occurs more commonly in males than females, with a ratio between 2:1 and 3:1. However, OCD has become more common among adolescent females as they become more active in sports. The adult form, which occurs in those who have reached skeletal maturity, is most commonly found in people 16 to 50 years old.

While OCD may affect any joint, the knee—specifically the medial femoral condyle in 75–85% of knee cases—tends to be the most commonly affected, and constitutes 75% of all cases. The elbow (specifically the capitulum of the humerus) is the second most affected joint with 6% of cases; the talar dome of the ankle represents 4% of cases. Less frequent locations include the patella, vertebrae, the femoral head, and the glenoid of the scapula.

While bone resorption is commonly associated with many diseases or joint problems, the term "osteolysis" generally refers to a problem common to artificial joint replacements such as total hip replacements, total knee replacements and total shoulder replacements. Osteolysis can also be associated with the radiographic changes seen in those with bisphosphonate-related osteonecrosis of the jaw.

There are several biological mechanisms which may lead to osteolysis. In total hip replacement, the generally accepted explanation for osteolysis involves wear particles (worn off the contact surface of the artificial ball and socket joint). As the body attempts to clean up these wear particles (typically consisting of plastic or metal), it triggers an autoimmune reaction which causes resorption of living bone tissue. Osteolysis has been reported to occur as early as 12 months after implantation and is usually progressive. This may require a revision surgery (replacement of the prosthesis).

Although osteolysis itself is clinically asymptomatic, it can lead to implant loosening or bone breakage, which in turn causes serious medical problems.

Heterotopic ossification (HO) is the process by which bone tissue forms outside of the skeleton.

Diffuse idiopathic skeletal hyperostosis (DISH) is a non-inflammatory spondyloarthropathy which predominantly affects the spine. It is characterized by ankylosis and enthesopathy (ossification of the ligaments and entheses). It most commonly affects the thoracic and thoraco-lumbar spine, but involvement is variable and can include the entire spine.

The ultimate cause for these conditions is unknown, but the most commonly cited cause factors are rapid growth, heredity, trauma (or overuse), anatomic conformation, and dietary imbalances; however, only anatomic conformation and heredity are well supported by scientific literature. The way that the disease is initiated has been debated. Although failure of chondrocyte differentiation, formation of a fragile cartilage, failure of blood supply to the growth cartilage, and bone necrosis all have been proposed as the starting point in the pathogenesis, recent literature strongly supports failure of blood supply to growth cartilage as most likely.

Osteolysis is an active resorption of bone matrix by osteoclasts and can be interpreted as the reverse of ossification. Although osteoclasts are active during the natural formation of healthy bone the term "osteolysis" specifically refers to a pathological process. Osteolysis often occurs in the proximity of a prosthesis that causes either an immunological response or changes in the bone's structural load. Osteolysis may also be caused by pathologies like bone tumors, cysts, or chronic inflammation.

The age range of patients with OPLL is from 32 to 81 years (mean = 53), with a male predominance. Prevalence is higher in those of Japanese or Asian ancestry (2-3.5%) and rarer in other racial groups (0.16%). Schizophrenia patients in Japan may have as high as 20% incidence.

A Salter–Harris fracture is a fracture that involves the epiphyseal plate or growth plate of a bone. It is a common injury found in children, occurring in 15% of childhood long bone fractures.

Osteochondrosis is a family of orthopedic diseases of the joint that occur in children and adolescents and in rapidly growing animals, particularly pigs, horses, dogs, and broiler chickens. They are characterized by interruption of the blood supply of a bone, in particular to the epiphysis, followed by localized bony necrosis, and later, regrowth of the bone. This disorder is defined as a focal disturbance of endochondral ossification and is regarded as having a multifactorial cause, so no one thing accounts for all aspects of this disease.

Most patients suffer from only mild symptoms. Symptoms typically last approximately 13 months. Of patients without myelopathy at initial presentation, only 29% of them will develop myelopathy within 30 years.

Multiple epiphyseal dysplasia (MED) encompasses a spectrum of skeletal disorders, most of which are inherited in an autosomal dominant form. However, there is an autosomal recessive form.

Associated genes include COL9A1, COL9A2, COL9A3, COMP, and MATN3.

Types include:

Fairbank's disease or multiple epiphyseal dysplasia (MED) is a rare genetic disorder (dominant form: 1 in 10,000 births) that affects the growing ends of bones. Long bones normally elongate by expansion of cartilage in the growth plate (epiphyseal plate) near their ends. As it expands outward from the growth plate, the cartilage mineralizes and hardens to become bone (ossification). In MED, this process is defective.

Ectopic calcification is a pathologic deposition of calcium salts in tissues or bone growth in soft tissues. This can be a symptom of hyperphosphatemia. Formation of osseous tissue in soft tissues such as the lungs, eyes, arteries, or other organs is known as ectopic calcification, dystrophic calcification, or ectopic ossification.

Calcific tendinitis is a form of tendinitis, a disorder characterized by deposits of hydroxyapatite (a crystalline calcium phosphate) in any tendon of the body, but most commonly in the tendons of the rotator cuff (shoulder), causing pain and inflammation. The condition is related to and may cause adhesive capsulitis ("frozen shoulder").

An accessory navicular bone is an accessory bone of the foot that occasionally develops abnormally in front of the ankle towards the inside of the foot. This bone may be present in approximately 2-21% of the general population and is usually asymptomatic. When it is symptomatic, surgery may be necessary.

Surgery can be performed at any age because it does not alter any other bones.

Symptoms of an accessory navicular bone may include plantar fasciitis, bunions and heel spurs.

Most (i.e. 80%) ossifications arise in the thigh or arm, and are caused by a premature return to activity after an injury. Other sites include intercostal spaces, erector spinae, pectoralis muscles, glutei, and the chest. On planar x-ray, hazy densities are sometimes noted approximately one month after injury, while the denser opacities eventually seen may not be apparent until two months have passed.

Absorption of calcium salts normally occurs in bony tissues and is facilitated by parathyroid hormone and vitamin D. However, increased amounts of parathyroid hormone in the blood result in the deposit of calcium in soft tissues. This can be an indication of hyperparathyroidism, arteriosclerosis, or trauma to tissues.

Calcification of muscle can occur after traumatic injury and is known as myositis ossificans. It can be recognized by muscle tenderness and loss of stretch in the affected area. To reduce the risk of calcification after an injury, initiate what is commonly known as "RICE" (rest, ice, compression, and elevation).

Removing the deposit/s either with open shoulder surgery or arthroscopic surgery are both difficult operations, but with high success rates (around 90%). About 10% require re-operation. If the deposit is large, then frequently the patient will require a rotator cuff repair to fix the defect left in the tendon when the deposit is removed or to reattach the tendon to the bone if the deposit was at the tendon insertion into the bone.

There are nine types of Salter–Harris fractures; types I to V as described by Robert B Salter and W Robert Harris in 1963, and the rarer types VI to IX which have been added subsequently:

- Type I – transverse fracture through the growth plate (also referred to as the "physis"): 6% incidence

- Type II – A fracture through the growth plate and the metaphysis, sparing the epiphysis: 75% incidence, takes approximately 2–3 weeks or more in the spine to heal.

- Type III – A fracture through growth plate and epiphysis, sparing the metaphysis: 8% incidence

- Type IV – A fracture through all three elements of the bone, the growth plate, metaphysis, and epiphysis: 10% incidence

- Type V – A compression fracture of the growth plate (resulting in a decrease in the perceived space between the epiphysis and metaphysis on x-ray): 1% incidence

- Type VI – Injury to the peripheral portion of the physis and a resultant bony bridge formation which may produce an angular deformity (added in 1969 by Mercer Rang)

- Type VII – Isolated injury of the epiphyseal plate (VII–IX added in 1982 by JA Ogden)

- Type VIII – Isolated injury of the metaphysis with possible impairment of endochondral ossification

- Type IX – Injury of the periosteum which may impair intramembranous ossification

Limited normal functions and movements are caused by osteochondromas growing slowly and inwardly. The majority of osteochondromas are symptomless and are found incidentally. Each individual with osteochondroma may experience symptoms differently and most of the time individuals will experience no symptoms at all. Some of the most common symptoms are a hard immobile painless palpable mass, adjacent muscle soreness, and pressure or irritation with heavy exercising.

Major symptoms arise when complications such as fractures, bone deformity or mechanical joint problems occur. If the occurrence of an osteochondroma is near a nerve or a blood vessel, the affected limb can experience numbness, weakness, loss of pulse or color change. Periodic changes in the blood flow can also take place. Approximately 20% of patients experiencing nerve compression commonly acknowledge vascular compression, arterial thrombosis, aneurysm, and pseudoaneurysm. Formation of pseudoaneurysm and venous thrombosis lead to claudication, pain, acute ischemia, and symptoms of phlebitis. If the tumor is found under a tendon, it can cause pain during movement causing restriction of joint motion. Pain can also occur due to bursal inflammation, swelling or fracture at the base of the tumor stalk. Some of the clinical signs and symptoms of malignant osteochondroma are pain, swelling, and mass enlargement.

As of 2017, approximately 800 cases of FOP have been confirmed worldwide making FOP one of the rarest diseases known. The estimated incidence of FOP is 0.5 cases per million people and affects all races.

Radiation therapy subsequent to the injury or as a preventive measure of recurrence may be applied but its usefulness is inconclusive. If the surgery performed next step in accordance with literature postoperative single low-dose radiation with 3 weeks of oral indomethacin regimen will be preventive for recurrence.