Once a diagnosis of dysmenorrhea is made, further workup is required to search for any secondary underlying cause of it, in order to be able to treat it specifically and to avoid the aggravation of a perhaps serious underlying cause.

Further work-up includes a specific medical history of symptoms and menstrual cycles and a pelvic exam. Based on results from these, additional exams and tests may be motivated, such as:

- Laboratory tests

- Gynecologic ultrasonography

- Laparoscopy may be required.

The diagnosis of dysmenorrhea is usually made simply on a medical history of menstrual pain that interferes with daily activities. However, there is no universally accepted gold standard technique for quantifying the severity of menstrual pains. Yet, there are quantification models, called "menstrual symptometrics", that can be used to estimate the severity of menstrual pains as well as correlate them with pain in other parts of the body, menstrual bleeding and degree of interference with daily activities.

The most common pain scale for quantification of endometriosis-related pain is the visual analogue scale (VAS); VAS and numerical rating scale (NRS) were the best adapted pain scales for pain measurement in endometriosis. For research purposes, and for more detailed pain measurement in clinical practice, VAS or NRS for each type of typical pain related to endometriosis (dysmenorrhea, deep dyspareunia and non-menstrual chronic pelvic pain), combined with the clinical global impression (CGI) and a quality of life scale, are used.

An area of research is the search for endometriosis markers.

In 2010 essentially all proposed biomarkers for endometriosis were of unclear medical use, although some appear to be promising. The one biomarker that has been in use over the last 20 years is CA-125. A 2016 review found that in those with symptoms of endometriosis and once ovarian cancer has been ruled out, a positive CA-125 may confirm the diagnosis. Its performance in ruling out endometriosis; however, is low. CA-125 levels appear to fall during endometriosis treatment, but has not shown a correlation with disease response.

Another review in 2011 identified several putative biomarkers upon biopsy, including findings of small sensory nerve fibers or defectively expressed β3 integrin subunit. It has been postulated a future diagnostic tool for endometriosis will consist of a panel of several specific and sensitive biomarkers, including both substance concentrations and genetic predisposition.

Adenomyosis can vary widely in the extent and location of its invasion within the uterus. As a result, there are no established pathognomonic features to allow for a definitive diagnosis of adenomyosis through non-invasive imaging. Nevertheless, non-invasive imaging techniques such as transvaginal ultrasonography (TVUS) and magnetic resonance imaging (MRI) can both be used to strongly suggest the diagnosis of adenomyosis, guide treatment options, and monitor response to treatment. Indeed, TVUS and MRI are the only two practical means available to establish a pre-surgical diagnosis.

Magnetic resonance imaging (MRI) provides slightly better diagnostic capability compared to TVUS, due to the increased ability of MRI to differentiate objectively between different types of soft tissue. This is possible with MRI's higher spatial and contrast resolution. Overall, it is estimated that MRI has a sensitivity of 74% and specificity of 91% for the detection of adenomyosis. Diagnosis through MRI focuses predominately upon investigating the junctional zone. The uterus will have a thickened junctional zone with darker/diminished signal on both T1 and T2 weighted sequences.

Three objective measures of the junctional zone can be used to diagnose adenomyosis.

1. A thickness of the junctional zone greater than 8–12 mm. Less than 8 mm is normal.

2. A junctional zone width being greater than 40% of the width of the myometrium.

3. Variability in the width of the junctional zone being greater than 5 mm.

Interspersed within the thickened, darker signal of the junctional zone, one will often see foci of hyperintensity (bright spots) on the T2 weighted scans representing small cystically dilatated glands or more acute sites of microhemorrhage.

MRI is limited by other factors, but not by calcified uterine fibroids (as is ultrasound). In particular, MRI is better able to differentiate adenomyosis from multiple small uterine fibroids.

The cause of the bleeding can often be discerned on the basis of the bleeding history, physical examination, and other medical tests as appropriate. The physical examination for evaluating vaginal bleeding typically includes visualization of the cervix with a speculum, a bimanual exam, and a rectovaginal exam. These are focused on finding the source of the bleeding and looking for any abnormalities that could cause bleeding. In addition, the abdomen is examined and palpated to ascertain if the bleeding is abdominal in origin. Typically a pregnancy test is performed as well. If bleeding was excessive or prolonged, a CBC may be useful to check for anemia. Abnormal endometrium may have to be investigated by a hysteroscopy with a biopsy or a dilation and curettage.

In an emergency or acute setting, vaginal bleeding can lead to hypovolemia.

The treatment will be directed at the cause. Hormonal bleeding problems during the reproductive years, if bothersome to the woman, are frequently managed by use of combined oral contraceptive pills.

In 2011, the International Federation of Gynaecology and Obstetrics (FIGO) recognized two systems designed to aid research, education, and clinical care of women with abnormal uterine bleeding (AUB) in the reproductive years.

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

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".

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.

A retroverted uterus is usually diagnosed during a routine pelvic examination or with an internal ultrasound.

It usually does not pose any medical problems, though it can be associated with dyspareunia (pain during sexual intercourse) and dysmenorrhea (pain during menstruation).

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.

Disorders of ovulation include oligoovulation and anovulation:

- Oligoovulation is infrequent or irregular ovulation (usually defined as cycles of ≥36 days or <8 cycles a year)

- Anovulation is absence of ovulation when it would be normally expected (in a post-menarchal, premenopausal woman). 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).

There are no laboratory tests or unique physical findings to verify the diagnosis of PMS. The three key features are:

- The woman's chief complaint is one or more of the emotional symptoms associated with PMS (most typically irritability, tension, or unhappiness). The woman does not have PMS if she only has physical symptoms, such as cramps or bloating.

- Symptoms appear predictably during the luteal (premenstrual) phase, reduce or disappear predictably shortly before or during menstruation, and remain absent during the follicular (preovulatory) phase.

- The symptoms must be severe enough to interfere with the woman's everyday life.

Mild PMS is common, and more severe symptoms would qualify as PMDD. PMS is not listed in the DSM-IV, unlike PMDD. To establish a pattern and determine if it is PMDD, a woman's physician may ask her to keep a prospective record of her symptoms on a calendar for at least two menstrual cycles. This will help to establish if the symptoms are, indeed, limited to the premenstrual time, predictably recurring, and disruptive to normal functioning. A number of standardized instruments have been developed to describe PMS, including the "Calendar of Premenstrual syndrome Experiences (COPE)", the "Prospective Record of the Impact and Severity of Menstruation (PRISM)", and the "Visual Analogue Scales (VAS)".

Other conditions that may better explain symptoms must be excluded. A number of medical conditions are subject to exacerbation at menstruation, a process called "menstrual magnification." These conditions may lead the woman to believe that she has PMS, when the underlying disorder may be some other problem, such as anemia, hypothyroidism, eating disorders and substance abuse. A key feature is that these conditions may also be present outside of the luteal phase. Conditions that can be magnified perimenstrually include depression or other affective disorders, migraine, seizure disorders, fatigue, irritable bowel syndrome, asthma, and allergies. Problems with other aspects of the female reproductive system must be excluded, including dysmenorrhea (pain during the menstrual period, rather than before it), endometriosis, perimenopause, and adverse effects produced by oral contraceptive pills.

The National Institute of Mental Health research definition compares the intensity of symptoms from cycle days 5 to 10 to the six-day interval before the onset of the menstrual period. To qualify as PMS, symptom intensity must increase at least 30% in the six days before menstruation. Additionally, this pattern must be documented for at least two consecutive cycles.

Diagnosis can be made using ultrasound or laparoscopy testing. The condition can also be diagnosed with a venogram, CT scan, or an MRI. Ultrasound is the diagnostic tool most commonly used. Recent research from a leading pelvic venous unit has suggested that Transvaginal Duplex Ultrasound scanning is the "Gold Standard" test for pelvic venous reflux. The same research group has shown that the size of the veins - as shown by venography and also used as the diagnostic criteria in CT and MRI - is not relevant and only Transvaginal Duplex Ultrasound shows the venous reflux that causes the problem.

Although hematometra can often be diagnosed based purely on the patient's history of amenorrhea and cyclic abdominal pain, as well as a palpable pelvic mass on examination, the diagnosis can be confirmed by ultrasound, which will show blood pooled in the uterus and an enlargement of the uterine cavity. A pyelogram or laparoscopy may assist in diagnosing any congenital disorder that is suspected to be the underlying cause of the hematometra.

Patients with a double uterus may need special attention during pregnancy as premature birth and malpresentation are common. Cesarean section was performed in 82% of patients reported by Heinonen.

Uterus didelphys, in certain studies, has also been found associated with higher rate of infertility, miscarriage, intrauterine growth retardation, and postpartum bleed.

A pelvic examination will typically reveal a double vagina and a double cervix. Investigations are usually prompted on the basis of such findings as well as when reproductive problems are encountered. Not all cases of uterus didelphys involve duplication of the cervix and vagina.

Helpful techniques to investigate the uterine structure are transvaginal ultrasonography and sonohysterography, hysterosalpingography, MRI, and hysteroscopy. More recently 3-D ultrasonography has been advocated as an excellent non-invasive method to evaluate uterine malformations.

Uterus didelphys is often confused with a complete uterine septum. Often more than one method of investigation is necessary to accurately diagnose the condition. Correct diagnosis is crucial as treatment for these two conditions is very different. Whereas most doctors recommend removal of a uterine septum, they generally concur that it is better not to operate on a uterus didelphys. In either case, a highly qualified reproductive endocrinologist should be consulted.

Pseudocyesis is not known to have a direct underlying physical cause and there are no general recommendations regarding treatment with medications. In some cases, however, the patient may be given medications for such symptoms as the cessation of menstruation. When some patients with pseudocyesis have underlying psychological problems, they should be referred to a psychotherapist for the treatment of these problems. It is important at the same time, however, for the treating professional not to minimize the reality of the patient's physical symptoms. The treatment that has had the most success is demonstrating to the patient that she is not really pregnant by the use of ultrasound or other imaging techniques.

Compared with the options available for treating sexual dysfunction in men (for whom results are concretely observable), those available for women are limited. For example, PDE5 inhibitors, oral medications for treating erectile dysfunction in men, have been tested for their ability to increase sexual responses such as arousal and orgasm in women—but no controlled trials have been done in women with SCI, and trials in other women yielded only inconclusive results. In theory, women's sexual response could be improved using a vacuum device made to draw blood into the clitoris, but few studies on treatments for sexual function in women with SCI have been carried out. There is a particular paucity of information outside the area of reproduction.

Without medical intervention, the male fertility rate after SCI is 5–14%, but the rate increases with treatments. Even with all available medical interventions, fewer than half of men with SCI can father children. Assisted insemination is usually required. As with erection, therapies used to treat infertility in uninjured men are used for those with SCI.

For anejaculation in SCI, the first-line method for sperm retrieval is penile vibratory stimulation (PVS). A high-speed vibrator is applied to the glans penis to trigger a reflex that causes ejaculation, usually within a few minutes. Reports of efficacy with PVS range from 15–88%, possibly due to differences in vibrator settings and experience of clinicians, as well as level and completeness of injury. Complete lesions strictly above Onuf's nucleus (S2–S4) are responsive to PVS in 98%, but complete lesions of the S2–S4 segments are not.

In case of failure with PVS, spermatozoa are sometimes collected by electroejaculation: an electrical probe is inserted into the rectum, where it triggers ejaculation. The success rate is 80–100%, but the technique requires anaesthesia and does not have the potential to be done at home that PVS has. Both PVS and electroejaculation carry a risk of autonomic dysreflexia, so drugs to prevent the condition can be given in advance and blood pressure is monitored throughout the procedures for those who are susceptible. Massage of the prostate gland and seminal vesicles is another method to retrieve stored sperm. If these methods fail to cause ejaculation or do not yield sufficient usable sperm, sperm can be surgically removed by testicular sperm extraction or percutaneous epididymal sperm aspiration. These procedures yield sperm in 86–100% of cases, but nonsurgical treatments are preferred.

Premature or spontaneous ejaculation is treated with antidepressants including selective serotonin reuptake inhibitors, which are known to delay ejaculation as a side effect.

Early treatment options include pain medication using nonsteroidal anti-inflammatory drugs, suppression of ovarian function, and alternative therapies such as acupuncture and physical therapy.

The surgical option involves stopping blood flow to the varicose veins using noninvasive surgical techniques such as a procedure called embolization. The procedure requires an overnight stay in hospital, and is done using local anesthetic. Patients report an 80% success rate, as measured by the amount of pain reduction experienced.

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.

The rate of pseudocyesis in the United States has declined significantly in the past century. In the 1940s there was one occurrence for approximately every 250 pregnancies. This rate has since dropped to between one and six occurrences for every 22,000 births. The average age of the affected woman is 33, though cases have been reported for girls as young as 6 and women as old as 79. More than two-thirds of women who experience pseudocyesis are married, and about one-third have been pregnant at least once.