A physical exam of the genitals is applied to ensure that there are no anatomical problems. The urine will be examined for the presence of semen. If there are no sperm in the urine, it may be due to damage to the prostate as a result of surgery or prior radiation therapy.

Diagnosis is usually by way of a urinalysis performed on a urine specimen that is obtained shortly after ejaculation. In cases of retrograde ejaculation, the specimen will contain an abnormal level of sperm.

Especially in case of "orgasmic anejaculation", anejaculation can often be confused with retrograde ejaculation, and they share some fundamental aspects of the cause. Urinalysis is used to distinguish between them.

The first-line method for sperm retrieval in men with spinal cord injury is "penile vibratory stimulation" (PVS). The penile vibratory stimulator is a plier-like device that is placed around glans penis to stimulate it by vibration. In case of failure with PVS, spermatozoa are sometimes collected by electroejaculation, or surgically by per cutaneous epididymal sperm aspiration (PESA) or testicular sperm extraction (TESE).

When deciding the appropriate treatment, it is important for the physician to distinguish PE as a "complaint" versus PE as a "syndrome". About 20 years ago, PE was classified into "lifelong PE" and "acquired PE". Recently, a new classification of PE was proposed based on controlled clinical and epidemiological stopwatch studies, and it included 2 other PE syndromes: "natural variable PE" and "premature-like ejaculatory dysfunction". Only individuals with lifelong PE with IELT shorter than 1–1.5 minutes should require medication as a first option, along with or without therapy. For those who fall into one of the other categories, treatment should consist of patient reassurance, behavior therapy, and/or psychoeducation to explain that irregular early ejaculation is a normal variation.

Several possible sub-classifications have been discussed, but none is in universal usage. "Primary premature ejaculation" refers to lifelong experience of the problem (since puberty), and "secondary premature ejaculation" reference to the problem beginning later in life. It has also been subdivided into "global premature ejaculation", when it occurs with all partners and contexts, and "situational premature ejaculation," when it occurs in some situations or with specific partners.

Low-volume, runny/fluid semen (oligospermia) or no semen at all (dry ejaculation/aspermia) are a logical consequence of an obstruction downstream of the seminal vesicles which contribute most to the volume of the semen. Usually, men will be able to observe a runny/fluid, low-volume semen by themselves during masturbation. Since the seminal vesicles contain a viscous, alkaline fluid rich in fructose, a chemical analysis of the semen of affected men will result in a low concentration of fructose and a low pH. A microscopic semen analysis will reveal aspermia/azoospermia.

In contrast, if both vasa deferentia are obstructed (which may be the result of intended sterilization), a semen analysis will also reveal aspermia/azoospermia, but an almost normal volume of the semen, since the efflux of the seminal vesicles is not hindered. This is because approx. 80% of the volume of the semen is the gel-like fluid originating from the seminal vesicles whereas the fraction from the testicles / epididymis, which contains the spermatozoa accounts for only 5–10% of the volume of the semen. In addition, if an obstruction of the vasa deferentia is the cause for the azoospermia, the concentration of fructose in the semen will also be normal, since the fructose comes primarily from the fluid stored in the seminal vesicles. If the seminal-vesicles contain spermatozoa, but the semen does not, the obstruction must be downstream of the seminal vesicles and the ejaculatory ducts are very likely to be obstructed, provided that other causes for a dry ejaculation/aspermia such as an retrograde ejaculation are ruled out.

Attempts are sometimes made to diagnose an ejaculatory duct obstruction by means of medical imaging, e.g. transrectal ultrasound or MRI, or by transrectal needle-aspiration of the seminal vesicles. However transrectal ultrasound has a relatively low sensitivity of approx. 50% and thus is only a tool to rule-out cysts in the region of the orifices but is not sufficient to rule out an obstruction of the ejaculatory ducts due to other causes. In approx. 50% of cases of unexplained low-volume azoospermia MRI and TRUS do not reveal any pathological findings, because it is difficult to see alterations in a narrowed, scarred duct with these methods. Due to the blockage of ejaculatory ducts, enlarged seminal vesicles are frequently seen in patients with ejaculatory duct obstructions. However, this is again neither a proof of an obstruction nor do normal-sized seminal vesicles rule-out an obstruction of the ejaculatory ducts. Since ejaculatory duct obstruction is a relatively rare cause of infertility, this possibility may be unfamiliar to some physicians, even some urologists.

Meditation has demonstrated effectiveness in case studies.

There is yet no reliable medication for delayed ejaculation. PDE5 inhibitors such as Viagra have little effect. In fact, Viagra has a delaying effect on ejaculation, possibly through additional effect in the brain or decrease of sensitivity in the head of the penis.

Therapy usually involves homework assignments and exercises intended to help a man get used to having orgasms through insertional intercourse, vaginal, anal, or oral, that is through the way to which he is not accustomed. Commonly, the couple is advised to go through three stages. At the first stage, a man masturbates in the presence of his partner. Sometimes, this is not an easy matter as a man may be used to having orgasms alone. After a man learns to ejaculate in the presence of his partner, the man's hand is replaced with the hand of his partner. In the final stage, the receptive partner inserts the insertive partner's penis into the partner's vagina, anus, or mouth as soon as the ejaculation is felt to be imminent. Thus, a man gradually learns to ejaculate inside the desired orifice by an incremental process.

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.

Several techniques have been developed and applied by sex therapists, including Kegel exercises (to strengthen the muscles of the pelvic floor) and Masters and Johnson's "stop-start technique" (to desensitize the man's responses) and "squeeze technique" (to reduce excessive arousal).

To treat premature ejaculation, Masters and Johnson developed the "squeeze technique", based on the Semans technique developed by Dr. James Semans in 1956. Men were instructed to pay close attention to their arousal pattern and learn to recognize how they felt shortly before their "point of no return", the moment ejaculation felt imminent and inevitable. Sensing it, they were to signal their partner, who squeezed the head of the penis between thumb and index finger, suppressing the ejaculatory reflex and allowing the man to last longer.

The squeeze technique worked, but many couples found it cumbersome. From the 1970s to the 1990s, sex therapists refined the Masters and Johnson approach, largely abandoning the squeeze technique and focused on a simpler and more effective technique called the "stop-start" technique. During intercourse, as the man senses he is approaching climax, both partners stop moving and remain still until the man's feelings of ejaculatory inevitability subside, at which point, they are free to resume active intercourse. To help the man increase awareness of his sexual experience, he is encouraged to create an excitement scale of 1-100. Successful completion of this scale will include paying attention to his heart rate, when (and if) he squeezes his inner thighs, and sensations in all parts of his body. By creating this scale, he will be more able to pace himself as he uses the "stop-start" technique.

In addition to the stop-start technique, other sexual adjustments help men develop and maintain ejaculatory control, among them: focus exercises, mind/body coordination exercises, masturbation exercises, deep breathing, and whole-body massage.

Sex therapists estimate that the refined last-longer program teaches effective ejaculatory control to 90 percent of men. The authors of one study concluded that sex therapy "has a remarkable therapeutic effect on premature ejaculation".

A method to treat ejaculatory duct obstruction is transurethral resection of the ejaculatory ducts (TURED). This operative procedure is relatively invasive, has some severe complications, and has led to natural pregnancies of their partners in approximately 20% of affected men. A disadvantage is the destruction of the valves at the openings of the ejaculatory ducts into the urethra such that urine may flow backwards into the seminal vesicles. Another, experimental approach is the recanalization of the ejaculatory ducts by transrectal or transurethral inserted balloon catheter. Though much less invasive and preserving the anatomy of the ejaculatory ducts, this procedure is probably not completely free of complications either and success rates are unknown. There is a clinical study currently ongoing to examine the success rate of recanalization of the ejaculatory ducts by means of balloon dilation.

Usually, affected men have a normal production of spermatozoa in their testicles, so that after spermatozoa were harvested directly from the testes e.g. by TESE, or the seminal vesicles (by needle aspiration) they and their partners are potentially candidates for some treatment options of assisted reproduction e.g. in-vitro fertilisation. Note that in this case, most of the treatment (e.g. ovarian stimulation and transvaginal oocyte retrieval) is transferred to the female partner.

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.

Some strategies suggested or proposed for avoiding male infertility include the following:

- Avoiding smoking as it damages sperm DNA

- Avoiding heavy marijuana and alcohol use.

- Avoiding excessive heat to the testes.

- Maintaining optimal frequency of coital activity: sperm counts can be depressed by daily coital activity and sperm motility may be depressed by coital activity that takes place too infrequently (abstinence 10–14 days or more).

- Wearing a protective cup and jockstrap to protect the testicles, in any sport such as baseball, football, cricket, lacrosse, hockey, softball, paintball, rodeo, motorcross, wrestling, soccer, karate or other martial arts or any sport where a ball, foot, arm, knee or bat can come into contact with the groin.

- Diet: Healthy diets (i.e. the Mediterranean diet) rich in such nutrients as omega-3 fatty acids, some antioxidants and vitamins, and low in saturated fatty acids (SFAs) and trans-fatty acids (TFAs) are inversely associated with low semen quality parameters. In terms of food groups, fish, shellfish and seafood, poultry, cereals, vegetables and fruits, and low-fat dairy products have been positively related to sperm quality. However, diets rich in processed meat, soy foods, potatoes, full-fat dairy products, coffee, alcohol and sugar-sweetened beverages and sweets have been inversely associated with the quality of semen in some studies. The few studies relating male nutrient or food intake and fecundability also suggest that diets rich in red meat, processed meat, tea and caffeine are associated with a lower rate of fecundability. This association is only controversial in the case of alcohol. The potential biological mechanisms linking diet with sperm function and fertility are largely unknown and require further study.

Ultrasonography of the scrotum is useful when there is a suspicion of some particular diseases. It may detect signs of testicular dysgenesis, which is often related to an impaired spermatogenesis and to a higher risk of testicular cancer. Scrotum ultrasonography may also detect testicular lesions suggestive of malignancy. A decreased testicular vascularization is characteristic of testicular torsion, whereas hyperemia is often observed in epididymo-orchitis or in some malignant conditions such as lymphoma and leukemia. Doppler ultrasonography useful in assessing venous reflux in case of a varicocele, when palpation is unreliable or in detecting recurrence or persistence after surgery, although the impact of its detection and surgical correction on sperm parameters and overall fertility is debated.

Dilation of the head or tail of the epididymis is suggestive of obstruction or inflammation of the male reproductive tract. Such abnormalities are associated with abnormalities in sperm parameters, as are abnormalities in the texture of the epididymis. Scrotal and transrectal ultrasonography (TRUS) are useful in detecting uni- or bilateral congenital absence of the vas deferens (CBAVD), which may be associated with abnormalities or agenesis of the epididymis, seminal vesicles or kidneys, and indicate the need for testicular sperm extraction. TRUS plays a key role in assessing azoospermia caused by obstruction, and detecting distal CBAVD or anomalies related to obstruction of the ejaculatory duct, such as abnormalities within the duct itself, a median cyst of the prostate (indicating a need for cyst aspiration), or an impairment of the seminal vesicles to become enlarged or emptied.

Several decades ago the medical community believed the majority of sexual dysfunction cases were related to psychological issues. Although this may be true for a portion of men, the vast majority of cases have now been identified as having a physical cause or correlation. If the sexual dysfunction is deemed to have a psychological component or cause, psychotherapy can help. Situational anxiety arises from an earlier bad incident or lack of experience. This anxiety often leads to development of fear towards sexual activity and avoidance. In return evading leads to a cycle of increased anxiety and desensitization of the penis. In some cases, erectile dysfunction may be due to marital disharmony. Marriage counseling sessions are recommended in this situation.

Lifestyle changes such as discontinuing smoking, drug or alcohol abuse can also help in some types of erectile dysfunction.

Several oral medications like Viagra, Cialis and Levitra have become available to help people with erectile dysfunction and have become first line therapy. These medications provide an easy, safe, and effective treatment solution for approximately 60% of men. In the rest, the medications may not work because of wrong diagnosis or chronic history.

Another type of medication that is effective in roughly 85% of men is called intracavernous pharmacotherapy and involves injecting a vasodilator drug directly into the penis in order to stimulate an erection. This method has an increased risk of priapism if used in conjunction with other treatments, and localized pain.

When conservative therapies fail, are an unsatisfactory treatment option, or are contraindicated for use, the insertion of a penile prosthesis, or penile implant, may be selected by the patient. Technological advances have made the insertion of a penile prosthesis a safe option for the treatment of erectile dysfunction which provides the highest patient and partner satisfaction rates of all available ED treatment options.

Pelvic floor physical therapy has been shown to be a valid treatment for men with sexual problems and pelvic pain.

Anejaculation is the pathological inability to ejaculate in males, with ("orgasmic") or without ("anorgasmic") orgasm.

Ultrasound examination is able to depict the tunica albuginea tear in the majority of cases (as a hypoechoic discontinuity in the normally echogenic tunica). In a study on 25 patients, Zare Mehrjardi et al. concluded that ultrasound is unable to find the tear just when it is located at the penile base. In their study magnetic resonance imaging (MRI) accurately diagnosed all of the tears (as a discontinuity in the normally low signal tunica on both T1- and T2-weighted sequences). They concluded that ultrasound should be considered as the initial imaging method, and MRI can be helpful in cases that ultrasound does not depict any tear but clinical suspicious for fracture is still high. In the same study, authors investigated accuracy of ultrasound and MRI for determining the tear location (mapping of fracture) in order to performing a tailored surgical repair. MRI was more accurate than ultrasound for this purpose, but ultrasound mapping was well correlated with surgical results in cases the tear was clearly visualized on ultrasound exam.

Although there are no approved pharmaceuticals for addressing female sexual disorders, several are under investigation for their effectiveness. A vacuum device is the only approved medical device for arousal and orgasm disorders. It is designed to increase blood flow to the clitoris and external genitalia. Women experiencing pain with intercourse are often prescribed pain relievers or desensitizing agents. Others are prescribed lubricants and/or hormone therapy. Many patients with female sexual dysfunction are often also referred to a counselor or therapist for psychosocial counseling.

Penile fracture is a medical emergency, and emergency surgical repair is the usual treatment. Delay in seeking treatment increases the complication rate. Non-surgical approaches result in 10–50% complication rates including erectile dysfunction, permanent penile curvature, damage to the urethra and pain during sexual intercourse, while operatively treated patients experience an 11% complication rate.

In some cases, retrograde urethrogram may be performed to rule out concurrent urethral injury.

Azoospermia is usually detected in the course of an infertility investigation. It is established on the basis of two semen analysis evaluations done at separate occasions (when the seminal specimen after centrifugation shows no sperm under the microscope) and requires a further work-up.

The investigation includes a history, a physical examination including a thorough evaluation of the scrotum and testes, laboratory tests, and possibly imaging. History includes the general health, sexual health, past fertility, libido, and sexual activity. Past exposure to a number of agents needs to be queried including medical agents like hormone/steroid therapy, antibiotics, 5-ASA inhibitors (sulfasalazine), alpha-blockers, 5 alpha-reductase inhibitors, chemotherapeutic agents, pesticides, recreational drugs (marijuana, excessive alcohol), and heat exposure of the testes. A history of surgical procedures of the genital system needs to be elicited. The family history needs to be assessed to look for genetic abnormalities.

Congenital absence of the vas deferens may be detectable on physical examination and can be confirmed by a transrectal ultrasound (TRUS). If confirmed genetic testing for cystic fibrosis is in order. Transrectal ultrasound can also assess azoospermia caused by obstruction, or anomalies related to obstruction of the ejaculatory duct, such as abnormalities within the duct itself, a median cyst of the prostate (indicating a need for cyst aspiration), or an impairment of the seminal vesicles to become enlarged or emptied.

Retrograde ejaculation is diagnosed by examining a postejaculatory urine for presence of sperm after making it alkaline and centifuging it.

Low levels of LH and FSH with low or normal testosterone levels are indicative of pretesticular problems, while high levels of gonadotropins indicate testicular problems. However, often this distinction is not clear and the differentiation between obstructive versus non-obstructive azoospermia may require a testicular biopsy. On the other hand, "In azoospermic men with a normal ejaculate volume, FSH serum level greater than two times the upper limit of the normal range is reliably diagnostic of dysfunctional spermatogenesis and, when found, a diagnostic testicular biopsy is usually unnecessary, although no consensus exists in this matter." But also, extremely high levels of FSH (>45 ID/mL) have been correlated with successful microdissection testicular sperm extraction.

Serum inhibin-B weakly indicates presence of sperm cells in the testes, raising chances for successfully achieving pregnancy through testicular sperm extraction (TESE), although the association is not very substantial, having a sensitivity of 0.65 (95% confidence interval [CI]: 0.56–0.74) and a specificity of 0.83 (CI: 0.64–0.93) for prediction the presence of sperm in the testes in non-obstructive azoospermia.

Seminal plasma proteins TEX101 and ECM1 were recently proposed for the differential diagnosis of azoospermia forms and subtypes, and for prediction of TESE outcome. Mount Sinai Hospital, Canada started clinical trial to test this hypothesis in 2016.

It is recommended that men primary hypopituitarism may be linked to a genetic cause, a genetic evaluation is indicated in men with azoospermia due to primary hypopituitarism. Azoospermic men with testicular failure are advised to undergo karyotype and Y-micro-deletion testing.

Achieving a pregnancy naturally may be a challenge if the male suffers from a low sperm count. However, chances are good if the female partner is fertile; many couples with this problem have been successful. Prognosis is more limited if there is a combination of factors that include sperm dysfunction and reduced ovarian reserve.

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.

Treatment takes place within the context of infertility management and needs also to consider the fecundity of the female partner. Thus the choices can be complex.

In a number of situations direct medical or surgical intervention can improve the sperm concentration, examples are use of FSH in men with pituitary hypogonadism, antibiotics in case of infections, or operative corrections of a hydrocele, varicocele, or vas deferens obstruction.

In most cases of oligospermia including its idiopathic form there is no direct medical or surgical intervention agreed to be effective. Empirically many medical approaches have been tried including clomiphene citrate, tamoxifen, HMG, FSH, HCG, testosterone, Vitamin E, Vitamin C, anti-oxidants, carnitine, acetyl-L-carnitine, zinc, high-protein diets. In a number of pilot studies some positive results have been obtained. Clomiphene citrate has been used with modest success. The combination of tamoxifen plus testosterone was reported to improve the sperm situation.

The use of carnitine showed some promise in a controlled trial in selected cases of male infertility improving sperm quality and further studies are needed.

In many situations, intrauterine inseminations are performed with success. In more severe cases IVF, or IVF - ICSI is done and is often the best option, specifically if time is a factor or fertility problems coexist on the female side.

The Low dose Estrogen Testosterone Combination Therapy may improve sperm count and motility in some men including severe oligospermia.

A retrospective postal survey of 396 men found that 4% had significant genital pain for more than one year that required surgical intervention.

Another study contacted 470 vasectomy patients and received 182 responses, finding that 18.7% of respondents experienced chronic genital pain with 2.2% of respondents experiencing pain that adversely affected quality of life.

The most robust study of post-vasectomy pain, according to the American Urology Association's Vasectomy Guidelines 2012 (amended 2015) found a rate of 14.7% reported new-onset scrotal pain at 7 months after vasectomy with 0.9% describing the pain as "quite severe and noticeably affecting their quality of life".

Some drugs such as trazodone may cause priapism as a side effect, in which case discontinuing the medication may give relief. Additionally, the condition can sometimes start only after the discontinuation of SSRIs. In some recorded cases, the syndrome was caused by or can cause a pelvic arterial-venous malformation with arterial branches to the penis or clitoris; surgical treatment was effective in this case.

In other situations where the cause is unknown or less easily treatable, the symptoms can sometimes be reduced by the use of antidepressants, antiandrogenic agents, and anaesthetising gels. Psychotherapy with cognitive reframing of the arousal as a healthy response may also be used.

More recently, the symptoms of the condition have also been linked with pudendal nerve entrapment. Regional nerve blocks and less common surgical intervention have demonstrated varying degrees of success in most cases. There is, however, no evidence for the long-term efficacy of surgical intervention.

In one recent case, serendipitous relief of symptoms was noted from treatment with varenicline, a treatment for nicotine addiction.