In certain cultures, deliberately inducing retrograde ejaculation by squeezing the urethra at the base or applying pressure to the perineum is done as a form of primitive male birth control ("coitus saxonicus"). An example is the practices of the Oneida Community. However, it is not considered a reliable method when compared to most modern types of birth control. Besides the common risks of pregnancy from pre-ejaculate and lack of protection from STDs, the technique itself can be hard to execute correctly during the act of coitus, especially if the male does not fully understand the anatomy involved.

Many doctors also do not recommend coitus saxonicus due to the risk of putting pressure on the pudendal nerve, which can cause numbness in the penis.

A malfunctioning bladder sphincter, leading to retrograde ejaculation, may be a result either of:

- Autonomic nervous system dysfunction. (Dysautonomia)

- Operation on the prostate. It is a common complication of transurethral resection of the prostate, a procedure in which prostate tissue is removed, slice by slice, through a resectoscope passed along the urethra.

It can also be caused by a retroperitoneal lymph node dissection for testicular cancer if nerve pathways to the bladder sphincter are damaged, with the resulting retrograde ejaculation being either temporary or permanent. Modern nerve-sparing techniques seek to reduce this risk; however, it may also occur as the result of Green Light Laser prostate surgery.

Surgery on the bladder neck accounted for about ten percent of the cases of retrograde ejaculation or anejaculation reported in a literature review.

Retrograde ejaculation is a common side effect of medications, such as tamsulosin, that are used to relax the muscles of the urinary tract, treating conditions such as benign prostatic hyperplasia. By relaxing the bladder sphincter muscle, the likelihood of retrograde ejaculation is increased.

The medications that mostly cause it are antidepressant and antipsychotic medication, as well as NRIs such as atomoxetine; patients experiencing this phenomenon tend to quit the medications.

Retrograde ejaculation can also be a complication of diabetes, especially in cases of diabetics with long term poor blood sugar control. This is due to neuropathy of the bladder sphincter. Post-pubertal males (aged 17 to 20 years) who experience repeated episodes of retrograde ejaculation are often diagnosed with urethral stricture disease shortly after the initial complaint arises. It is currently not known whether a congenital malformation of the bulbous urethra is responsible, or if pressure applied to the base of the penis or perineum immediately preceding ejaculatory inevitability may have inadvertently damaged the urethra. This damage is most often seen within 0.5 cm of the ejaculatory duct (usually distal to the duct).

Retrograde ejaculation can also result from pinching closed the urethral opening, to avoid creating a mess upon ejaculation (known as "Hughes' technique").

The causes of premature ejaculation are unclear. Many theories have been suggested, including that PE was the result of masturbating quickly during adolescence to avoid being caught, of performance anxiety, of an unresolved Oedipal conflict, of passive-aggressiveness, and having too little sex; but there is little evidence to support any of these theories.

Several physiological mechanisms have been hypothesized to contribute to causing premature ejaculation including serotonin receptors, a genetic predisposition, elevated penile sensitivity, and nerve conduction atypicalities.

The nucleus paragigantocellularis of the brain has been identified as having involvement in ejaculatory control. Scientists have long suspected a genetic link to certain forms of premature ejaculation. In one study, 91 percent of men who have had premature ejaculation for their entire lives also had a first-relative with lifelong premature ejaculation. Other researchers have noted that men who have premature ejaculation have a faster neurological response in the pelvic muscles.

PE may be caused by prostatitis or as a drug side effect.

Medical conditions that can cause delayed ejaculation include hypogonadism, thyroid disorders, pituitary disorders such as Cushing's disease, prostate surgery outcome, and drug and alcohol use. Difficulty in achieving orgasm can also result from pelvic surgery that involved trauma to pelvic nerves responsible for orgasm. Some men report a lack of sensation in the nerves of the glans penis, which may or may not be related to external factors, including a history of circumcision.

Delayed ejaculation is a possible side effect of certain medications, including selective serotonin reuptake inhibitors (SSRIs), opiates such as morphine, methadone, or oxycodone, many benzodiazepines such as Valium, certain antipsychotics, and antihypertensives.

Psychological and lifestyle factors have been discussed as potential contributors, including insufficient sleep, distraction due to worry, distraction from the environment, anxiety about pleasing their partner and anxiety about relationship problems.

One proposed cause of delayed ejaculation is adaptation to a certain masturbatory technique. The sensations a man feels when masturbating may bear little resemblance to the sensations he experiences during intercourse. Factors such as pressure, angle and grip during masturbation can make for an experience so different from sex with a partner that the ability to ejaculate is reduced or eliminated.

On the same note, it may be the visual factor present in masturbation that may delay vaginal ejaculation. As the sensation during masturbation is intrinsically linked with the visual input of a sexual model, be it male or female, the diminished view during sex may result in the loss of that link, and as such, delay ejaculation in the man. A possible cure for this may be a better view of the partner during intercourse.

Premature ejaculation is a prevalent sexual dysfunction in men; however, because of the variability in time required to ejaculate and in partners' desired duration of sex, exact prevalence rates of PE are difficult to determine. In the "Sex in America" surveys (1999 and 2008), University of Chicago researchers found that between adolescence and age 59, approximately 30% of men reported having experienced PE at least once during the previous 12 months, whereas about 10 percent reported erectile dysfunction (ED). Although ED is men's most prevalent sex problem after age 60, and may be more prevalent than PE overall according to some estimates, premature ejaculation remains a significant issue that, according to the survey, affects 28 percent of men age 65–74, and 22 percent of men age 75–85. Other studies report PE prevalence ranging from 3 percent to 41 percent of men over 18, but the great majority estimate a prevalence of 20 to 30 percent—making PE a very common sex problem.

There is a common misconception that younger men are more likely to suffer premature ejaculation and that its frequency decreases with age. Prevalence studies have indicated, however, that rates of PE are constant across age groups.

The numbers of women with SCI giving birth and having healthy babies are increasing. Around a half to two-thirds of women with SCI report they might want to have children, and 14–20% do get pregnant at least once. Although female fertility is not usually permanently reduced by SCI, there is a stress response that can happen immediately post-injury that alters levels of fertility-related hormones in the body. In about half of women, menstruation stops after the injury but then returns within an average of five months—it returns within a year for a large majority. After menstruation returns, women with SCI become pregnant at a rate close to that of the rest of the population.

Pregnancy is associated with greater-than-normal risks in women with SCI, among them increased risk of deep vein thrombosis, respiratory infection, and urinary tract infection. Considerations exist such as maintaining proper positioning in a wheelchair, prevention of pressure sores, and increased difficulty moving due to weight gain and changes in center of balance. Assistive devices may need to be altered and medications changed.

For women with injuries above T6, a risk during labor and delivery that threatens both mother and fetus is autonomic dysreflexia, in which the blood pressure increases to dangerous levels high enough to cause potentially deadly stroke. Drugs such as nifedipine and captopril can be used to manage an episode if it occurs, and epidural anesthesia helps although it is not very reliable in women with SCI. Anesthesia is used for labor and delivery even for women without sensation, who may only experience contractions as abdominal discomfort, increased spasticity, and episodes of autonomic dysreflexia. Reduced sensation in the pelvic area means women with SCI usually have less painful delivery; in fact, they may fail to realize when they go into labor. If there are deformities in the pelvis or spine caesarian section may be necessary. Babies of women with SCI are more likely to be born prematurely, and, premature or not, they are more likely to be small for their gestational time.

It can depend on one or more of several causes, including:

- Sexual inhibition

- Pharmacological inhibition. They include mostly antidepressant and antipsychotic medication, and the patients experiencing that tend to quit them

- Autonomic nervous system

- Prostatectomy - surgical removal of the prostate.

- Ejaculatory duct obstruction

- Spinal cord injury causes sexual dysfunction including anejaculation. The rate of being able to ejaculate varies with the type of lesion, as detailed in the table at right.

- old age

Anejaculation, especially the "orgasmic" variant, is usually indistinguishable from retrograde ejaculation. However, a negative urinalysis measuring no abnormal presence of spermatozoa in the urine will eliminate a retrograde ejaculation diagnosis.

Thus, if the affected man has the sensations and involuntary muscle-contractions of an orgasm but no or very low-volume semen, ejaculatory duct obstruction is another possible underlying pathology of anejaculation.

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).

Erectile dysfunction from vascular disease is usually seen only amongst elderly individuals who have atherosclerosis. Vascular disease is common in individuals who have diabetes, peripheral vascular disease, hypertension and those who smoke. Any time blood flow to the penis is impaired, erectile dysfunction is the end result.

Hormone deficiency is a relatively rare cause of erectile dysfunction. In individuals with testicular failure like in Klinefelter syndrome, or those who have had radiation therapy, chemotherapy or childhood exposure to mumps virus, the testes may fail and not produce testosterone. Other hormonal causes of erectile failure include brain tumors, hyperthyroidism, hypothyroidism or disorders of the adrenal gland.

Structural abnormalities of the penis like Peyronie's disease can make sexual intercourse difficult. The disease is characterized by thick fibrous bands in the penis which leads to a deformed-looking penis.

Drugs are also a cause of erectile dysfunction. Individuals who take drugs to lower blood pressure, uses antipsychotics, antidepressants, sedatives, narcotics, antacids or alcohol can have problems with sexual function and loss of libido.

Priapism is a painful erection that occurs for several hours and occurs in the absence of sexual stimulation. This condition develops when blood gets trapped in the penis and is unable to drain out. If the condition is not promptly treated, it can lead to severe scarring and permanent loss of erectile function. The disorder occurs in young men and children. Individuals with sickle-cell disease and those who abuse certain medications can often develop this disorder.

Men with SCI rank the ability to father children among their highest concerns relating to sexuality. Male fertility is reduced after SCI, due to a combination of problems with erections, ejaculation, and quality of the semen. As with other types of sexual response, ejaculation can be psychogenic or reflexogenic, and the level of injury affects a man's ability to experience each type. As many as 95% of men with SCI have problems with ejaculation (anejaculation), possibly due to impaired coordination of input from different parts of the nervous system. Erection, orgasm, and ejaculation can each occur independently, although the ability to ejaculate seems linked to the quality of the erection, and the ability to orgasm is linked to the ejaculation facility. Even men with complete injuries may be able to ejaculate, because other nerves involved in ejaculation can effect the response without input from the spinal cord. In general, the higher the level of injury, the more physical stimulation the man needs to ejaculate. Conversely, premature or spontaneous ejaculation can be a problem for men with injuries at levels T12–L1. It can be severe enough that ejaculation is provoked by thinking a sexual thought, or for no reason at all, and is not accompanied by orgasm.

Most men have a normal sperm count, but a high proportion of sperm are abnormal; they are less motile and do not survive as well. The reason for these abnormalities is not known, but research points to dysfunction of the seminal vesicles and prostate, which concentrate substances that are toxic to sperm. Cytokines, immune proteins which promote an inflammatory response, are present at higher concentrations in semen of men with SCI, as is platelet-activating factor acetylhydrolase; both are harmful to sperm. Another immune-related response to SCI is the presence of a higher number of white blood cells in the semen.

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.

There are many factors which may result in a person experiencing a sexual dysfunction. These may result from emotional or physical causes. Emotional factors include interpersonal or psychological problems, which can be the result of depression, sexual fears or guilt, past sexual trauma, and sexual disorders, among others.

Sexual dysfunction is especially common among people who have anxiety disorders. Ordinary anxiousness can obviously cause erectile dysfunction in men without psychiatric problems, but clinically diagnosable disorders such as panic disorder commonly cause avoidance of intercourse and premature ejaculation. Pain during intercourse is often a comorbidity of anxiety disorders among women.

Physical factors that can lead to sexual dysfunctions include the use of drugs, such as alcohol, nicotine, narcotics, stimulants, antihypertensives, antihistamines, and some psychotherapeutic drugs. For women, almost any physiological change that affects the reproductive system—premenstrual syndrome, pregnancy and the postpartum period, menopause—can have an adverse effect on libido. Injuries to the back may also impact sexual activity, as can problems with an enlarged prostate gland, problems with blood supply, or nerve damage (as in sexual dysfunction after spinal cord injuries). Diseases such as diabetic neuropathy, multiple sclerosis, tumors, and, rarely, tertiary syphilis may also impact the activity, as could the failure of various organ systems (such as the heart and lungs), endocrine disorders (thyroid, pituitary, or adrenal gland problems), hormonal deficiencies (low testosterone, other androgens, or estrogen) and some birth defects.

Pelvic floor dysfunction is also a physical and underlying cause of many sexual dysfunctions.

In the context of heterosexual relationships, one of the main reasons for the decline in sexual activity among these couples is the male partner experiencing erectile dysfunction. This can be very distressing for the male partner, causing poor body image, and it can also be a major source of low desire for these men. In aging women, it is natural for the vagina to narrow and become atrophied. If a woman has not been participating in sexual activity regularly (in particular, activities involving vaginal penetration) with her partner, if she does decide to engage in penetrative intercourse, she will not be able to immediately accommodate a penis without risking pain or injury. This can turn into a vicious cycle, often leading to female sexual dysfunction.

According to Emily Wentzell, American culture has anti-aging sentiments that have caused sexual dysfunction to become "an illness that needs treatment" instead of viewing it as the natural part of the aging process it is. Not all cultures seek treatment; for example, a population of men living in Mexico often accept erectile dysfunction as a normal part of their maturing sexuality

There is increasing evidence that the harmful products of tobacco smoking may damage the testicles and kill sperm, but their effect on male fertility is not clear. Some governments require manufacturers to put warnings on packets. Smoking tobacco increases intake of cadmium, because the tobacco plant absorbs the metal. Cadmium, being chemically similar to zinc, may replace zinc in the DNA polymerase, which plays a critical role in sperm production. Zinc replaced by cadmium in DNA polymerase can be particularly damaging to the testes.

Pre-testicular factors refer to conditions that impede adequate support of the testes and include situations of poor hormonal support and poor general health including:

- Hypogonadotropic hypogonadism due to various causes

- Obesity increases the risk of hypogonadotropic hypogonadism. Animal models indicate that obesity causes leptin insensitivity in the hypothalamus, leading to decreased Kiss1 expression, which, in turn, alters the release of gonadotropin-releasing hormone (GnRH).

- Undiagnosed and untreated coeliac disease (CD). Coeliac men may have reversible infertility. Nevertheless, CD can present with several non-gastrointestinal symptoms that can involve nearly any organ system, even in the absence of gastrointestinal symptoms. Thus, the diagnosis may be missed, leading to a risk of long-term complications. In men, CD can reduce semen quality and cause immature secondary sex characteristics, hypogonadism and hyperprolactinaemia, which causes impotence and loss of libido. The giving of gluten free diet and correction of deficient dietary elements can lead to a return of fertility. It is likely that an effective evaluation for infertility would best include assessment for underlying celiac disease, both in men and women.

- Drugs, alcohol

- Strenuous riding (bicycle riding, horseback riding)

- Medications, including those that affect spermatogenesis such as chemotherapy, anabolic steroids, cimetidine, spironolactone; those that decrease FSH levels such as phenytoin; those that decrease sperm motility such as sulfasalazine and nitrofurantoin

- Genetic abnormalities such as a Robertsonian translocation

The human breast cancer susceptibility gene 2 (BRCA2) is employed in homologous recombinational repair of DNA damages during meiosis. A common single-nucleotide polymorphism of BRCA2 is associated with severe oligospermia.

Men with mild oligospermia (semen concentration of 15 million to 20 million sperm/ml) were studied for an association of sperm DNA damage with life style factors. A significant association was found between sperm DNA damage and factors such as age, obesity and occupational stress.

Pre-testicular factors refer to conditions that impede adequate support of the testes and include situations of poor hormonal support and poor general health including:

- Hypogonadism due to various causes

- Drugs, alcohol, smoking

- Strenuous riding (bicycle riding, horseback riding)

- Medications, including androgens.

Aspermia is the complete lack of semen with ejaculation (not to be confused with azoospermia, the lack of sperm cells in the semen). It is associated with infertility.

One of the causes of aspermia is retrograde ejaculation, which can be brought on by excessive drug use, or as a result of prostate surgery. It can also be caused by alpha blockers such as tamsulosin and silodosin.

Another cause of aspermia is ejaculatory duct obstruction, which may result in a complete lack of or a very low-concentration semen (oligospermia), in which the semen contains only the secretion of accessory prostate glands downstream to the orifice of the ejaculatory ducts.

Aspermia can be caused by androgen deficiency. This can be the result of absence of puberty, in which the prostate gland and seminal vesicles (which are the main sources of semen) remain small due to lack of androgen exposure and do not produce seminal fluid, or of treatment for prostate cancer, such as maximal androgen blockade.

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".

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.

There is not enough known about persistent genital arousal disorder to definitively pinpoint a cause. Medical professionals think it is caused by an irregularity in sensory nerves, and note that the disorder has a tendency to strike post-menopausal women, or those who have undergone hormonal treatment.

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.

Odynorgasmia, or painful ejaculation, is a physical syndrome described by pain or burning sensation of the urethra or perineum during or following ejaculation. Causes include infections associated with urethritis, prostatitis, epididymitis, as well as use of anti-depressants.

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.

Although widely discussed, there had been scant information in medical research literature aside from a brief article by Chalett and Nerenberg in "Pediatrics" 2000, which found little formal data existed regarding the condition, but concluded that "[t]he treatment is sexual release, or perhaps straining to move a very heavy object — in essence doing a Valsalva maneuver."

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