Causes of HAIR-AN syndrome are not yet discovered or are not specifically known. But depending on some tests and data collected, HAIR-AN syndrome is thought to be caused by "both genetic and environmental" conditions or factors. And although it might be uncertain of what particularly caused HAIR-AN syndrome, one could just go and find out how hyperandrogenism, insulin resistance and acanthosis nigricans are caused, as these three are the leading contributors to HAIR-AN syndrome, which indirectly signifies that HAIR-AN syndrome is caused by these three. Knowing the cause of these three might provide one with some useful data that connects or links with the causes of HAIR-AN syndrome. SAHA syndrome is also taken in consider among the source that cause HAIR-An syndrome.

A diagnosis of PCOS suggests an increased risk of the following:

- Endometrial hyperplasia and endometrial cancer (cancer of the uterine lining) are possible, due to overaccumulation of uterine lining, and also lack of progesterone resulting in prolonged stimulation of uterine cells by estrogen. It is not clear whether this risk is directly due to the syndrome or from the associated obesity, hyperinsulinemia, and hyperandrogenism.

- Insulin resistance/Type II diabetes. A review published in 2010 concluded that women with PCOS have an elevated prevalence of insulin resistance and type II diabetes, even when controlling for body mass index (BMI). PCOS also makes a woman, particularly if obese, prone to gestational diabetes.

- High blood pressure, in particular if obese or during pregnancy

- Depression and anxiety

- Dyslipidemia – disorders of lipid metabolism — cholesterol and triglycerides. Women with PCOS show a decreased removal of atherosclerosis-inducing remnants, seemingly independent of insulin resistance/Type II diabetes.

- Cardiovascular disease, with a meta-analysis estimating a 2-fold risk of arterial disease for women with PCOS relative to women without PCOS, independent of BMI.

- Strokes

- Weight gain

- Miscarriage

- Sleep apnea, particularly if obesity is present

- Non-alcoholic fatty liver disease, again particularly if obesity is present

- Acanthosis nigricans (patches of darkened skin under the arms, in the groin area, on the back of the neck)

- Autoimmune thyroiditis

Early diagnosis and treatment may reduce the risk of some of these, such as type 2 diabetes and heart disease.

The risk of ovarian cancer and breast cancer is not significantly increased overall.

While hyperandrogenism in women is caused by external factors, it can also appear from natural causes.

The preferable way to diagnose the presence of this syndrome would be to use the help of clinical tests and medical reports after the tests and examinations. Now being aware of the subject that HAIR-AN syndrome is caused by genetic, environmental factors and also the hyperandogenism, insulin resistance and acanthosis nigricans, some of the way we could diagnosis this syndrome is by looking for signs in the body for symptoms leading to relate to those key contributors discussed above.

According to studies HAIR-AN is to be found in 1% to 3% women possessing hyperandrogenism. It is an established concept in physiopathology that the androgen in the female body is produced by the stromal ovarian cells, when stimulated by the LH and HCG. The observed activity of these cells was elevated by insulin, and later was found to be used as a determining element to find how severe the hirsutism was. Physicians must look for obesity, as it is also a diagnostic factor in many possible cases.

The prevalence of PCOS depends on the choice of diagnostic criteria. The World Health Organization estimates that it affects 116 million women worldwide as of 2010 (3.4% of women). One community-based prevalence study using the Rotterdam criteria found that about 18% of women had PCOS, and that 70% of them were previously undiagnosed.

Ultrasonographic findings of polycystic ovaries are found in 8–25% of normal women. 14% women on oral contraceptives are found to have polycystic ovaries. Ovarian cysts are also a common side effect of intrauterine devices (IUDs).

Even though hyperandrogenism is not common in men, there has been studies done to look at the effects of high levels of testosterone in male bodies. A study have shown that even though many of the male participates did not have a behavior changes due to the increased levels of testosterone, there were cases where the participants had instances of uncharacteristic aggression. High levels of testosterone in male has not been seen to have a direct impact on their personality, but within those studies, there have been cases of sudden aggression within the male participants.

Early puberty is believed to put girls at higher risk of sexual abuse, unrelated to pedophilia because the child has developed secondary sex characteristics; however, a causal relationship is, as yet, inconclusive. Early puberty also puts girls at a higher risk for teasing or bullying, mental health disorders and short stature as adults. Helping children control their weight is suggested to help delay puberty. Early puberty additionally puts girls at a "far greater" risk for breast cancer later in life. Girls as young as 8 are increasingly starting to menstruate, develop breasts and grow pubic and underarm hair; these "biological milestones" typically occurred only at 13 or older in the past. African-American girls are especially prone to early puberty. There are theories debating the trend of early puberty, but the exact causes are not known.

Though boys face fewer problems upon early puberty than girls, early puberty is not always positive for boys; early sexual maturation in boys can be accompanied by increased aggressiveness due to the surge of hormones that affect them. Because they appear older than their peers, pubescent boys may face increased social pressure to conform to adult norms; society may view them as more emotionally advanced, although their cognitive and social development may lag behind their appearance. Studies have shown that early maturing boys are more likely to be sexually active and are more likely to participate in risky behaviours.

Hirsutism can be caused by either an increased level of androgens, the male hormones, or an oversensitivity of hair follicles to androgens. Male hormones such as testosterone stimulate hair growth, increase size and intensify the growth and pigmentation of hair. Other symptoms associated with a high level of male hormones include acne, deepening of the voice, and increased muscle mass. The condition is called hyperandrogenism.

Growing evidence implicates high circulating levels of insulin in women for the development of hirsutism. This theory is speculated to be consistent with the observation that obese (and thus presumably insulin resistant hyperinsulinemic) women are at high risk of becoming hirsute. Further, treatments that lower insulin levels will lead to a reduction in hirsutism.

It is speculated that insulin, at high enough concentration, stimulates the ovarian theca cells to produce androgens. There may also be an effect of high levels of insulin to activate insulin-like growth factor 1 (IGF-1) receptor in those same cells. Again, the result is increased androgen production.

Signs that are suggestive of an androgen-secreting tumor in a patient with hirsutism is rapid onset, virilization and palpable abdominal mass.

The following are conditions and situations that have been associated with hyperandrogenism and hence hirsutism in women:

- Hyperinsulinemia (insulin excess) or hypoinsulinemia (insulin deficiency or resistance as in diabetes).

- Ovarian cysts such as in polycystic ovary syndrome (PCOS), the most common cause in women.

- Ovarian tumors such as granulosa tumors, thecomas, Sertoli–Leydig cell tumors (androblastomas), and gynandroblastomas, as well as ovarian cancer.

- Hyperthecosis.

- Pregnancy.

- Adrenal gland tumors, adrenocortical adenomas, and adrenocortical carcinoma, as well as adrenal hyperplasia due to pituitary adenomas (as in Cushing's syndrome).

- hCG-secreting tumors

- Inborn errors of steroid metabolism such as in congenital adrenal hyperplasia, most commonly caused by 21-hydroxylase deficiency.

- Acromegaly and gigantism (growth hormone and IGF-1 excess), usually due to pituitary tumors.

- Use of certain medications such as androgens/anabolic steroids, phenytoin, and minoxidil.

Causes of hirsutism not related to hyperandrogenism include:

- Porphyria cutanea tarda.

- Minoxidil

Many causes of early puberty are somewhat unclear, though girls who have a high-fat diet and are not physically active or are obese are more likely to physically mature earlier. "Obese girls, defined as at least 10 kilograms (22 pounds) overweight, had an 80 percent chance of developing breasts before their ninth birthday and starting menstruation before age 12 – the western average for menstruation is about 12.7 years." Exposure to chemicals that mimic estrogen (known as xenoestrogens) is a possible cause of early puberty in girls. Bisphenol A, a xenoestrogen found in hard plastics, has been shown to affect sexual development. "Factors other than obesity, however, perhaps genetic and/or environmental ones, are needed to explain the higher prevalence of early puberty in black versus white girls." While more girls are increasingly entering puberty at younger ages, new research indicates that some boys are actually starting later (delayed puberty). "Increasing rates of obese and overweight children in the United States may be contributing to a later onset of puberty in boys, say researchers at the University of Michigan Health System."

High levels of beta-hCG in serum and cerebrospinal fluid observed in a 9-year-old boy suggest a pineal gland tumor. The tumor is called a "chorionic gonadotropin secreting pineal tumor". Radiotherapy and chemotherapy reduced tumor and beta-hCG levels normalized.

In a study using neonatal melatonin on rats, results suggest that elevated melatonin could be responsible for some cases of early puberty.

Familial cases of idiopathic central precocious puberty (ICPP) have been reported, leading researchers to believe there are specific genetic modulators of ICPP. Mutations in genes such as LIN28, and LEP and LEPR, which encode leptin and the leptin receptor, have been associated with precocious puberty. The association between LIN28 and puberty timing was validated experimentally in vivo, when it was found that mice with ectopic overexpression of LIN28 show an extended period of pre-pubertal growth and a significant delay in puberty onset.

Mutations in the kisspeptin (KISS1) and its receptor, KISS1R (also known as GPR54), involved in GnRH secretion and puberty onset, are also thought to be the cause for ICPP However, this is still a controversial area of research, and some investigators found no association of mutations in the LIN28 and KISS1/KISS1R genes to be the common cause underlying ICPP.

The gene MKRN3, which is a maternally imprinted gene, was first cloned by Jong et al in 1999. MKRN3 was originally named Zinc finger protein 127. It is located on human chromosome 15 on the long arm in the Prader-Willi syndrome critical region2, and has since been identified as a cause of premature sexual development or CPP. The identification of mutations in MKRN3 leading to sporadic cases of CPP has been a significant contribution to better understanding the mechanism of puberty. MKRN3 appears to act as a "brake" on the central hypothalamic-pituitary access. Thus, loss of function mutations of the protein allow early activation of the GnRH pathway and cause phenotypic CPP. Patients with a MKRN3 mutation all display the classic signs of CCP including early breast and testes development, increased bone aging and elevated hormone levels of GnRH and LH.

Hirsutism affects members of any gender, since rising androgen levels can cause excessive body hair, particularly in locations where women normally do not develop terminal hair during puberty (chest, abdomen, back, and face). The medical term for excessive hair growth that affects any gender is hypertrichosis.

Androgen deficiency is not usually checked for diagnosis in healthy women.

Hypoandrogenism is caused primarily by either dysfunction, failure, or absence of the gonads ("hypergonadotropic") or impairment of the hypothalamus or pituitary gland ("hypogonadotropic"), which in turn can be caused by a multitude of different stimuli, including genetic conditions (e.g., GnRH/gonadotropin insensitivity and enzymatic defects of steroidogenesis), tumors, trauma, surgery, autoimmunity, radiation, infections, toxins, drugs, and many others. Alternatively, it may be the result of conditions such as androgen insensitivity syndrome or hyperestrogenism. More simply, old age may also be a factor in the development of hypoandrogenism, as androgen levels decline with age.

Crandall syndrome is a very rare congenital disorder characterised by progressive sensorineural hearing loss, hair loss associated with pili torti, and hypogonadism demonstrated through low levels of luteinising hormone and growth hormone. It is thought to be an autosomal recessive disorder closely related to Björnstad syndrome which presents similarly but without hypogonadism.

The condition was first reported by B. F. Crandall in 1973.

Hypertrichosis is often mistakenly classified as hirsutism. Hirsutism is a type of hypertrichosis exclusive to women and children, resulting from an excess of androgen-sensitive hair growth. Patients with hirsutism exhibit patterns of adult male hair growth. Chest and back hair are often present on women with hirsutism.

Hirsutism is both congenital and acquired. It is linked to excessive male hormones in women, thus symptoms may include acne, deepening of the voice, irregular menstrual periods, and the formation of a more masculine body shape. Increases in androgen (male hormone) levels are the primary cause of most hirsutism cases. If caused by increased levels of androgens, it can be treated with medications that reduce androgen levels. Some birth control pills and spironolactone reduce androgen levels.

The exact genetic mutation that causes congenital circumscribed, localized, and nevoid hypertrichosis is unknown.

Male pattern hair loss is believed to be due to a combination of genetics and the male hormone dihydrotestosterone. The cause in female pattern hair remains unclear.

Research is looking into connections between hair loss and other health issues. While there has been speculation about a connection between early-onset male pattern hair loss and heart disease, a review of articles from 1954 to 1999 found no conclusive connection between baldness and coronary artery disease. The dermatologists who conducted the review suggested further study was needed.

Environmental factors are under review. A 2007 study indicated that smoking may be a factor associated with age-related hair loss among Asian men. The study controlled for age and family history, and found statistically significant positive associations between moderate or severe male pattern hairloss and smoking status.

Vertex baldness is associated with an increased risk of coronary heart disease (CHD) and the relationship depends upon the severity of baldness, while frontal baldness is not. Thus, vertex baldness might be a marker of CHD and is more closely associated with atherosclerosis than frontal baldness.

Genetic forms of localized autosomal recessive hypotrichosis include:

Hypotrichosis ("" + "" + "") is a condition of abnormal hair patterns, predominantly loss or reduction. It occurs, most frequently, by the growth of vellus hair in areas of the body that normally produce terminal hair. Typically, the individual's hair growth is normal after birth, but shortly thereafter the hair is shed and replaced with sparse, abnormal hair growth. The new hair is typically fine, short and brittle, and may lack pigmentation. Baldness may be present by the time the subject is 25 years old.

Hypotrichosis is a common feature of Hallermann–Streiff syndrome as well as others. It can also be used to describe the lack of hair growth due to chemotherapy.

The opposite of hypotrichosis is hypertrichosis, where terminal hair (thick) grows in areas that would otherwise normally have vellus hair (thin), for example abnormally thick facial hair growth in women.

CCCA tends to present itself in the 20s and progresses over 20–30 years. One should consider this diagnosis in African Americans with what appears to be a female-pattern hair loss.

Sabinas brittle hair syndrome, also called Sabinas syndrome or brittle hair-mental deficit syndrome, is an autosomal recessive congenital disorder affecting the integumentary system.

This condition is self-limiting. Improvements in grooming techniques and in environmental conditions will correct the abnormality.

Wiedemann–Rautenstrauch (WR) syndrome , also known as neonatal progeroid syndrome, is an autosomal recessive progeroid syndrome.

WR was first reported by Rautenstrauch and Snigula in 1977; and the earliest reports made subsequently have been by Wiedemann in 1979, by Devos in 1981, and Rudin in 1988. There have been over 30 cases of WR.

WR is associated with abnormalities in bone maturation, and lipids and hormone metabolism. Affected individuals exhibit intrauterine and postnatal growth retardation, leading to short stature and an aged appearance from birth. They have physical abnormalities including a large head (macrocephaly), sparse hair, prominent scalp veins, inward-folded eyelid (entropion), widened anterior fontanelles, hollow cheeks (malar hypoplasia), general loss of fat tissues under the skin (lipoatrophy), delayed tooth eruption, abnormal hair pattern (hypotrichosis), beaked nose, mild to severe mental retardation and dysmorphism.

Marfan lipodystrophy syndrome (MFLS) has sometimes been confused with Wiedemann–Rautenstrauch syndrome, since the Marfanoid features are progressive and sometimes incomplete. MFLS is caused by mutations near the 3'-terminus of "FBN1" that cause a deficiency of the protein hormone asprosin and progeroid-like symptoms with reduced subcutaneous white adipose tissue.

GAPO syndrome is caused by a deletion in both copies of the ANTXR1 gene, which encodes Anthrax Toxin Receptor 1. This gene is critical for the creation of actin, and its disruption inhibits proper function of the actin network. As a result, individuals with GAPO syndrome have a buildup of extracellular matrix, and degraded cell adhesions. The alteration can occur in the form of nonsense mutations or mutations which alter the splice sites, and result in alternative RNA splicing, leading to synthesis of a different or modified protein. In humans, the ANTXR1 gene is located on Chromosome 2 and has 22 exons.

GAPO syndrome is inherited in an autosomal recessive fashion, and requires both parents to pass on the mutant genotype. Since this mutation is so rare, most confirmed cases have a history of ancestral inbreeding.

There is currently no cure for GAPO syndrome, but some options are available to reduce the symptoms. Nearsightedness, which affects some sufferers of the disease, can be treated by corrective lenses. Unfortunately, optic atrophy as a result of degradation of the optic nerve (common with GAPO syndrome) cannot be corrected. Corticosteroids have been proposed as a treatment for optic nerve atrophy, but their effectiveness is disputed, and no steroid based treatments are currently available.