Breastfeeding is a common cause of secondary amenorrhoea, and often the condition lasts for over six months. Breastfeeding typically lasts longer than lactational amenorrhoea, and the duration of amenorrhoea varies depending on how often a women breastfeeds. Lactational amenorrhoea has been advocated as a method of family planning, especially in developing countries where access to other methods of contraception may be limited. Breastfeeding is said to prevent more births in the developing world than any other method of birth control or contraception. Lactational amenorrhoea is 98% percent effective as a method of preventing pregnancy in the first six months postpartum.

In the Western world, the typical age of menopause (last period from natural causes) is between 40 and 61 and the average age for last period is 51 years. The average age of natural menopause in Australia is 51.7 years. In India and the Philippines, the median age of natural menopause is considerably earlier, at 44 years.

In rare cases, a woman's ovaries stop working at a very early age, ranging anywhere from the age of puberty to age 40. This is known as premature ovarian failure and affects 1 to 2% of women by age 40.

Undiagnosed and untreated coeliac disease is a risk factor for early menopause. Coeliac disease can present with several non-gastrointestinal symptoms, in the absence of gastrointestinal symptoms, and most cases escape timely recognition and go undiagnosed, leading to a risk of long-term complications. A strict gluten-free diet reduces the risk. Women with early diagnosis and treatment of coeliac disease present a normal duration of fertile life span.

Women who have undergone hysterectomy with ovary conservation go through menopause on average 3.7 years earlier than the expected age. Other factors that can promote an earlier onset of menopause (usually 1 to 3 years early) are smoking cigarettes or being extremely thin.

Certain medications, particularly contraceptive medications, can induce amenorrhoea in a healthy woman. The lack of menstruation usually begins shortly after beginning the medication and can take up to a year to resume after stopping a medication. Hormonal contraceptives that contain only progestogen like the oral contraceptive Micronor, and especially higher-dose formulations like the injectable Depo Provera commonly induce this side-effect. Extended cycle use of combined hormonal contraceptives also allow suppression of menstruation. Patients who use and then cease using contraceptives like the combined oral contraceptive pill may experience secondary amenorrhoea as a withdrawal symptom. The link is not well understood, as studies have found no difference in hormone levels between women who develop amenorrhoea as a withdrawal symptom following the cessation of OCOP use and women who experience secondary amenorrhoea because of other reasons. New contraceptive pills, like continuous oral contraceptive pills (OCPs) which do not have the normal 7 days of placebo pills in each cycle, have been shown to increase rates of amenorrhoea in women. Studies show that women are most likely to experience amenorrhoea after 1 year of treatment with continuous OCP use.

The use of opiates (such as heroin) on a regular basis has also been known to cause amenorrhoea in longer term users.

Anti-psychotic drugs used to treat schizophrenia have been known to cause amenorrhoea as well. New research suggests that adding a dosage of Metformin to an anti-psychotic drug regimen can restore menstruation. Metformin decreases resistance to the hormone insulin, as well as levels of prolactin, testosterone, and lutenizing hormone (LH). Metformin also decreases the LH/FSH ratio. Results of the study on Metformin further implicate the regulation of these hormones as a main cause of secondary amenorrhoea.

Menopause confers:

- A possible but contentious increased risk of atherosclerosis. The risk of acute myocardial infarction and other cardiovascular diseases rises sharply after menopause, but the risk can be reduced by managing risk factors, such as tobacco smoking, hypertension, increased blood lipids and body weight.

- Increased risk of osteopenia, osteoporosis, and accelerated lung function decline.

Women who experience menopause before 45 years of age have an increased risk of heart disease, death, and impaired lung function.

For most women, alteration of menstrual periods is the principal indication of chronic anovulation. Ovulatory menstrual periods tend to be regular and predictable in terms of cycle length, duration and heaviness of bleeding, and other symptoms. Ovulatory periods are often accompanied by midcycle symptoms such as mittelschmerz or premenstrual symptoms. In contrast, anovulation usually manifests itself as irregularity of menstrual periods, that is, unpredictable variability of intervals, duration, or bleeding. Anovulation can also cause cessation of periods (secondary amenorrhea) or excessive bleeding (dysfunctional uterine bleeding). Mittelschmerz and premenstrual symptoms tend to be absent or reduced when a woman is anovulatory.

This accounts for around 10-15% of all cases of anovulation. The ovaries can stop working in about 5% of cases. This may be because the ovaries do not contain eggs. However, a complete blockage of the ovaries is rarely a cause of infertility. Blocked ovaries can start functioning again without a clear medical explanation. In some cases, the egg may have matured properly, but the follicle may have failed to burst (or the follicle may have burst without releasing the egg). This is called luteinised unruptured follicle syndrome (LUFS). Physical damage to the ovaries, or ovaries with multiple cysts, may affect their ability to function. This is called ovarian . Patients who are suffering from Stein-Leventhal syndrome (also referred to as polycystic ovary syndrome, or PCOS) can also suffer from anovulation. Up to 90% of cases of anovulation are caused by PCOS; this syndrome is usually hereditary.

Weight loss or anorexia can also cause hormonal imbalance, leading to irregular ovulation (dysovulation). It is possible that this mechanism evolved to protect the mother’s health. A pregnancy where the mother is weak could pose a risk to the baby’s and mother’s health. On the other hand, excess weight can also create ovarian dysfunctions. Dr Barbieri of Harvard Medical School has indicated that cases of anovulation are quite frequent in women with a BMI (body mass index) over 27 /. Unfortunately, not only does excess weight have a negative impact on ovulation itself, but also on treatment efficacy and outcomes of ART (assisted reproductive technique).

Oligomenorrhea can be a result of prolactinomas (adenomas of the anterior pituitary). It may be caused by thyrotoxicosis, hormonal changes in perimenopause, Prader–Willi syndrome, and Graves disease.

"Endurance exercises such as running or swimming can affect the reproductive physiology of women athletes. Female runners, swimmers and ballet dancers menstruate infrequently in comparison to nonatheletic women of comparable age or not at all (amenorrhea). The degree of menstrual abnormality is directly proportional to the intensity of the exercise. For example, Malina et al., (1978) have shown menstrual irregularity is more common, and more severe among tennis players than among golfers" (modified by a student paper written by A. Lord)

Breastfeeding has been linked to irregularity of menstrual cycles due to hormones that delay ovulation.

Women with polycystic ovary syndrome (PCOS) are also likely to suffer from oligomenorrhea. PCOS is a condition in which excessive androgens (male sex hormones) are released by the ovaries. Women with PCOS show menstrual irregularities that range from oligomenorrhea and amenorrhea, to very heavy, irregular periods. The condition affects about 6% of premenopausal women.

Eating disorders can result in oligomenorrhea. Although menstrual disorders are most strongly associated with Anorexia nervosa, Bulimia nervosa may also result in oligomenorrhea or amenorrhea. There is some controversy regarding the mechanism for the menstrual dysregulation, since amenorrhea may sometimes precede substantial weight loss in some anorexics. Some researchers hypothesize that some as-yet unrecognized neuroendocrine phenomenon may be involved; the menstrual irregularities may be related to the biological undergirding of the disorders, rather than a result of nutritional deficiencies.

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.

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).

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.

Dysmenorrhea (or dysmenorrhoea), cramps or painful menstruation, involves menstrual periods that are accompanied by either sharp, intermittent pain or dull, aching pain, usually in the pelvis or lower abdomen.

Exercise induced amenorrhoea occurs in 5-25% of athletes and 1.8% of the general population. The incidence is higher in marathon runners and is more frequent in women who weigh less and were slightly younger . Exercise amenorrhoea has also been reported in ballet dancers, cyclists, swimmers and those involved in non-weight bearing sports .

A menstrual disorder is an abnormal condition in a woman's menstrual cycle.

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.

Because hyperandrogenism can appear as a symptom of numerous different genetic and medical conditions, it is difficult to make a general statement on whether hyperandrogenic symptoms can be passed from parent to offspring. However, a collection of the conditions with hyperandrogenic symptoms, including polycystic ovary syndrome, have been observed as hereditary in certain cases. One potential cause of polycystic ovary syndrome is maternal hyperandrogenism, where the hormonal irregularities of the mother can affect the development of the child during gestation, resulting in the passing of polycystic ovary syndrome from mother to child.

Oligomenorrhea (or oligomenorrhoea) is infrequent (or, in occasional usage, very light) menstruation. More strictly, it is menstrual periods occurring at intervals of greater than 35 days, with only four to nine periods in a year. Menstrual periods should have been regularly established before the development of infrequent flow. The duration of such events may vary.

There occurs a suppression in the generation of gonadotropin releasing hormone (GnRH). The secretion of GnRH normally occurs in a pulsatile fashion, every 60 to 90 minutes. This is absent in exercise amenorrhoea. The function of GnRH is to stimulate the secretion of leutinizing hormone (LH) and follicle stimulating hormone (FSH). As a result, LH and to a certain extent FSH are secreted in low quantities. These hormones are necessary for normal menstruation, and result in amenorrhoea if not secreted in adequate quantities .

Prolactin secretion in the pituitary is normally suppressed by the brain chemical dopamine. Drugs that block the effects of dopamine at the pituitary or deplete dopamine stores in the brain may cause the pituitary to secrete prolactin. These drugs include the major tranquillizers (phenothiazines), trifluoperazine (Stelazine), and haloperidol (Haldol); antipsychotic medications, such as risperidone and quetiapine; metoclopramide (Reglan), domperidone, cisapride used to treat gastro-oesophageal reflux; medication-induced nausea (such as cancer drugs); and, less often, alpha-methyldopa and reserpine, used to control hypertension; and estrogens and TRH. The sleep drug ramelteon (Rozerem) also increases the risk of hyperprolactinaemia. A benzodiazepine analog, etizolam, can also increase the risk of hyperprolactinaemia. In particular, the dopamine antagonists metoclopramide and domperidone are both powerful prolactin stimulators and have been used to stimulate breast milk secretion for decades. However, since prolactin is antagonized by dopamine and the body depends on the two being in balance, the risk of prolactin stimulation is generally present with all drugs that deplete dopamine, either directly or as a rebound effect.

The cause is not entirely clear. Risk factors include having a family history of the condition.

Excessive menstruation between puberty and 19 years of age is called puberty menorrhagia. Excessive menstruation is defined as bleeding over 80 ml per menstrual period or lasting more than 7 days. The most common cause for puberty menorrhagia is dysfunctional uterine bleeding. The other reasons are idiopathic thrombocytopenic purpura, hypothyroidism, genital tuberculosis, polycystic ovarian disease, leukemia and coagulation disorders. The most common physiological reason for puberty menorrhagia is the immaturity of hypothalamic-pituitary-ovarian axis, leading to inadequate positive feedback and sustained high estrogen levels. Most patients present with anemia due to excessive blood loss.

The patient is assessed with a thorough medical history, physical examination (to look for features of anemia), gynaecological examination (to rule out local causes) and laboratory investigations (to rule out coagulopathies and malignancy). It is mandatory to exclude pregnancy. The treatment is determined based on the cause of menorrhagia. In case of puberty menorrhagia due to immaturity of hypothalamic axis, hormonal therapy is beneficial. Treatment for blood loss should be done simultaneously with iron therapy in mild to moderate blood loss and blood transfusion in severe blood loss.

Physiological (i.e., non-pathological) causes include: pregnancy, breastfeeding, and mental stress.

Dysmenorrhea is estimated to affect approximately 25% of women. Reports of dysmenorrhea are greatest among individuals in their late teens and 20s, with reports usually declining with age. The prevalence in adolescent females has been reported to be 67.2% by one study and 90% by another. It has been stated that there is no significant difference in prevalence or incidence between races. Yet, a study of Hispanic adolescent females indicated a high prevalence and impact in this group. Another study indicated that dysmenorrhea was present in 36.4% of participants, and was significantly associated with lower age and lower parity. Childbearing is said to relieve dysmenorrhea, but this does not always occur. One study indicated that in nulliparous women with primary dysmenorrhea, the severity of menstrual pain decreased significantly after age 40. A questionnaire concluded that menstrual problems, including dysmenorrhea, were more common in females who had been sexually abused.

A survey in Norway showed that 14 percent of females between the ages of 20 to 35 experience symptoms so severe that they stay home from school or work. Among adolescent girls, dysmenorrhea is the leading cause of recurrent short-term school absence.

Some factors associated with endometriosis include:

- not having had yet given birth

- prolonged exposure to estrogen - for example, in late menopause or early menarche

- obstruction of menstrual outflow - for example, in Müllerian anomalies

Several studies have investigated the potential link between exposure to dioxins and endometriosis, but the evidence is equivocal and potential mechanisms are poorly understood. A 2004 review of studies of dioxin and endometriosis concluded that "the human data supporting the dioxin-endometriosis association are scanty and conflicting", and a 2009 follow-up review also found that there was "insufficient evidence" in support of a link between dioxin exposure and women developing endometriosis. A 2008 review concluded that more work was needed, stating that "although preliminary work suggests a potential involvement of exposure to dioxins in the pathogenesis of endometriosis, much work remains to clearly define cause and effect and to understand the potential mechanism of toxicity".

Irregular cycles or irregular periods is an abnormal variation in length of menstrual cycles. A female usually experiences cycle length variations of up to eight days between the shortest and longest cycle lengths. Lengths ranging between eight and 20 days are considered moderately irregular. Variation of 21 days or more is considered very irregular.

Alternatively, a single menstruation period may be defined as irregular if it is shorter than 21 days or longer than 36 days. If they are regularly shorter than 21 days or longer than 36 (or 35) days, the condition is termed polymenorrhea or oligomenorrhea, respectively.