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

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".

Dysmenorrhea can be classified as either primary or secondary based on the absence or presence of an underlying cause. Secondary dysmenorrhea is dysmenorrhea which is associated with an existing condition.

The most common cause of secondary dysmenorrhea is endometriosis, which can be visually confirmed by laparoscopy in approximately 70% of adolescents with dysmenorrhea.

Other causes of secondary dysmenorrhea include leiomyoma, adenomyosis, ovarian cysts, and pelvic congestion.

Unequal leg length might hypothetically be one of the contributors, as it may contribute to a tilted pelvis, which may cause lower back pain, which in turn may be mistaken for menstrual pain, as women with lower back pain experience increased pain during their periods.

Other skeletal abnormalities, such as scoliosis (sometimes caused by spina bifida) might be possible contributors as well.

Adenomyosis itself can cause infertility issues, however, fertility can be improved if the adenomyosis has resolved following hormone therapies like levonorgestrel therapy. The discontinuation of medication or removal of IUD can be timed to be coordinated with fertility treatments. There has also been one report of a successful pregnancy and healthy birth following high-frequency ultrasound ablation of adenomyosis.

Preterm labour and premature rupture of membranes both occur more frequently in women with adenomyosis.

In sub-fertile women who received in-vitro fertilization (IVF), women with adenomyosis were less likely to become pregnant and subsequently more likely to experience a miscarriage. Given this, it is encouraged to screen women for adenomyosis by TVUS or MRI before starting assisted reproduction treatments (ART).

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

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.

Adenomyosis is a benign but often progressing condition. It is advocated that adenomyosis poses no increased risk for cancer development. However, both entities could coexist and the endometrial tissue within the myometrium could harbor endometrioid adenocarcinoma, with potentially deep myometrial invasion. As the condition is estrogen-dependent, menopause presents a natural cure. Ultrasound features of adenomyosis will still be present after menopause. People with adenomyosis are also more likely to have uterine fibroids or endometriosis.

Endometrial atrophy, uterine fibroids, and endometrial cancer are common causes of postmenopausal vaginal bleeding.

Vaginal bleeding occurs during 15-25% of first trimester pregnancies. Of these, half go on to miscarry and half bring the fetus to term. There are a number of causes including rupture of a small vein on the outer rim of the placenta. It can also herald a miscarriage or ectopic pregnancy, which is why urgent ultrasound is required to separate the two causes. Bleeding in early pregnancy may be a sign of a threatened or incomplete miscarriage.

In the second or third trimester a placenta previa (a placenta partially or completely overlying the cervix) may bleed quite severely. Placental abruption is often associated with uterine bleeding as well as uterine pain.

Examples of congenital abnormalities of the reproductive system include:

- Kallmann syndrome - Genetic disorder causing decreased functioning of the sex hormone-producing glands caused by a deficiency or both testes from the scrotum.

- Androgen insensitivity syndrome - A genetic disorder causing people who are genetically male (i.e. XY chromosome pair) to develop sexually as a female due to an inability to utilize androgen.

- Intersexuality - A person who has genitalia and/or other sexual traits which are not clearly male or female.

Rarely, a sharply tilted uterus is due to a disease such as endometriosis, an infection or prior surgery. Although this may make it more challenging for the sperm to reach the egg, conception can still occur. A tipped uterus will usually right itself during the 10th to 12th week of pregnancy. Rarely (1 in 3000 to 8000 pregnancies) a tipped uterus will cause painful and difficult urination, and can cause severe urinary retention. Treatment for this condition (called "incarcerated uterus") includes manual anteversion of the uterus, and usually requires intermittent or continuous catheter drainage of the bladder until the problem is rectified or spontaneously resolves by the natural enlargement of the uterus, which brings it out of the tipped position. In addition to manual anteversion and bladder drainage, treatment of urinary retention due to retroverted uterus can require the use of a pessary, or even surgery, but often is as simple as having the pregnant mother sleep on her stomach for a day or two, to allow the retroverted uterus to move forward.

If a uterus does not right itself, it may be labeled "persistent".

It is also known that disruption of the endocrine system by certain chemicals adversely affects the development of the reproductive system and can cause vaginal cancer. Many other reproductive diseases have also been link to exposure to synthetic and environmental chemicals. Common chemicals with known links to reproductive disorders include: lead, dioxins and dioxin-like compounds, styrene, toluene, BPA (Bisphenol A) and pesticides.

Hematometra develops when the uterus becomes distended with blood secondary to obstruction or atresia of the lower reproductive tract—the uterus, cervix or vagina—which would otherwise provide an outflow for menstrual blood. It is most commonly caused by congenital abnormalities, including imperforate hymen, transverse vaginal septum or vaginal hypoplasia. Other causes are acquired, such as cervical stenosis, intrauterine adhesions, endometrial cancer, and cervical cancer.

Additionally, hematometra may develop as a complication of uterine or cervical surgery such as endometrial ablation, where scar tissue in the endometrium can "wall off" sections of endometrial glands and stroma causing blood to accumulate in the uterine cavity. It can also develop after abortion, as well as after childbirth. It can also develop after female genital mutilation.

In the United States, uterus didelphys is reported to occur in 0.1–0.5% of women. It is difficult to know the exact occurrence of this anomaly, as it may go undetected in the absence of medical and reproductive complications.

In most cases, a retroverted uterus is genetic and is perfectly normal but there are other factors that can cause the uterus to be retroverted. Some cases are caused by pelvic surgery, pelvic adhesions, endometriosis, fibroids, pelvic inflammatory disease, or the labor of childbirth.

A number of twin gestations have occurred where each uterus carried its pregnancy separately. A recent example occurred on February 26, 2009, when Sarah Reinfelder of Sault Ste. Marie, Michigan delivered two healthy, although seven weeks premature, infants by cesarean section at Marquette General Hospital. It is possible that the deliveries occur at different times, thus the delivery interval could be days or even weeks.

Hematometra is usually treated by surgical cervical dilation to drain the blood from the uterus. Other treatments target the underlying cause of the hematometra; for example, a hysteroscopy may be required to resect adhesions that have developed following a previous surgery. If the cause of the hematometra is unclear, a biopsy of endometrial tissue can be taken to test for the presence of a neoplasm (cancer). Antibiotics may be given as prophylaxis against the possibility of infection.

Pelvic congestion syndrome (also known as pelvic vein incompetence) is a chronic medical condition in women caused by varicose veins in the lower abdomen. The condition causes chronic pain, often manifesting as a constant dull ache, which can be aggravated by standing. Early treatment options include pain medication, alternative therapies such as acupuncture, and suppression of ovarian function. Surgery can be done using noninvasive transcatheter techniques to embolize the varicose veins. Up to 80% of women obtain relief using this method.

The condition can occur as a result of pregnancy or for unknown reasons. The presence of estrogen in the body causes vasodilation, which can result in the accumulation of blood in the veins in the pelvic area. Estrogen can weaken the vein walls, leading to the changes that cause varicosities. Up to 15% of all women have varicose veins in the abdominal area, but not all have symptoms.

Women with this condition experience a constant pain that may be dull and aching, but is occasionally more acute. The pain is worse at the end of the day and after long periods of standing, and sufferers get relief when they lie down. The pain is worse during or after sexual intercourse, and can be worse just before the onset of the menstrual period.

Women with pelvic congestion syndrome have a larger uterus and a thicker endometrium. 56% of women manifest cystic changes to the ovaries, and many report other symptoms, such as dysmenorrhea, back pain, vaginal discharge, abdominal bloating, mood swings or depression, and fatigue.

Endometrial polyps usually occur in women in their 40s and 50s. Endometrial polyps occur in up to 10% of women. It is estimated that they are present in 25% of women with abnormal vaginal bleeding.

Up to 80% women of child-bearing age report having some symptoms prior to menstruation. These symptoms qualify as PMS in 20 to 30% of women and in three to eight percent are severe.

PMS is generally a stable diagnosis, with susceptible women experiencing the same symptoms at the same intensity near the end of each cycle for years. Treatment for specific symptoms is usually effective.

Even without treatment, symptoms tend to decrease in perimenopausal women. However, women who experience PMS or PMDD are more likely to have significant symptoms associated with menopause, such as hot flashes.

Endometrial polyps are usually benign although some may be precancerous or cancerous. About 0.5% of endometrial polyps contain adenocarcinoma cells. Polyps can increase the risk of miscarriage in women undergoing IVF treatment. If they develop near the fallopian tubes, they may lead to difficulty in becoming pregnant. Although treatments such as hysteroscopy usually cure the polyp concerned, recurrence of endometrial polyps is frequent. Untreated, small polyps may regress on their own.

Adenomyoma is a tumor ("-oma") including components derived from glands ("adeno-") and muscle ("-my-"). It is a type of complex and mixed tumor.