The female sexual response system is complex and even today, not fully understood. The most prevalent of female sexual dysfunctions that have been linked to menopause include lack of desire and libido; these are predominantly associated with hormonal physiology. Specifically, it is the decline in serum estrogens that causes these changes in sexual functioning. Androgen depletion may also play a role, but currently this is less clear. The hormonal changes that take place during the menopausal transition have been suggested to affect women's sexual response through several mechanisms, some more conclusive than others.

Whether or not aging directly affects women's sexual functioning during menopause is another area of controversy. However, many studies, including Hayes and Dennerstein's critical review, have demonstrated that aging has a powerful impact on sexual function and dysfunction in women, specifically in the areas of desire, sexual interest, and frequency of orgasm. In addition, Dennerstien and colleagues found that the primary predictor of sexual response throughout menopause is prior sexual functioning. This means that it is important to understand how the physiological changes in men and women can affect their sexual desire. Despite the seemingly negative impact that menopause can have on sexuality and sexual functioning, sexual confidence and well-being can improve with age and menopausal status. Furthermore, the impact that a relationship status can have on quality of life is often underestimated.

Testosterone, along with its metabolite dihydrotestosterone, is extremely important to normal sexual functioning in men and women. Dihydrotestosterone is the most prevalent androgen in both men and women. Testosterone levels in women at age 60 are, on average, about half of what they were before the women were 40. Although this decline is gradual for most women, those who’ve undergone bilateral oophorectomy experience a sudden drop in testosterone levels; this is because the ovaries produce 40% of the body's circulating testosterone.

Sexual desire has been related to three separate components: drive, beliefs and values, and motivation. Particularly in postmenopausal women, drive fades and is no longer the initial step in a woman's sexual response (if it ever was).

Secondary anorgasmia is close to 50% among males undergoing prostatectomy; 80% among radical prostatectomies. This is a serious adverse result because radical prostatectomies are usually given to younger males who are expected to live more than 10 years. At more advanced ages, the prostate is less likely to grow during that person's remaining lifetime. This is generally caused by damage to the primary nerves serving the penile area, which pass near the prostate gland. Removal of the prostate frequently damages or even completely removes these nerves, making sexual response unreasonably difficult.

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.

The condition is sometimes classified as a psychiatric disorder. However, it can also be caused by medical problems such as diabetic neuropathy, multiple sclerosis, genital mutilation, complications from genital surgery, pelvic trauma (such as from a straddle injury caused by falling on the bars of a climbing frame, bicycle or gymnastics beam), hormonal imbalances, total hysterectomy, spinal cord injury, cauda equina syndrome, uterine embolisation, childbirth trauma (vaginal tearing through the use of forceps or suction or a large or unclosed episiotomy), vulvodynia and cardiovascular disease.

A common cause of situational anorgasmia, in both men and women, is the use of anti-depressants, particularly selective serotonin reuptake inhibitors (SSRIs). Though reporting of anorgasmia as a side effect of SSRIs is not precise, studies have found that 17–41% of users of such medications are affected by some form of sexual dysfunction.

Another cause of anorgasmia is opiate addiction, particularly to heroin.

About 15% of women report difficulties with orgasm, and as many as 10% of women in the United States have never climaxed. Only 29% of women always have orgasms with their partner.

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.

Delayed ejaculation can be "mild" (men who still experience orgasm during intercourse, but only under certain conditions), "moderate" (cannot ejaculate during intercourse, but can during fellatio or manual stimulation), "severe" (can ejaculate only when alone), or "most severe" (cannot ejaculate at all). All forms may result in a sense of sexual frustration.

Freudian theory postulated that rapid ejaculation was a symptom of underlying neurosis. It stated that the man suffers unconscious hostility toward women, so he ejaculates rapidly, which satisfies him but frustrates his lover, who is unlikely to experience orgasm that quickly. Freudians claimed that premature ejaculation could be cured using psychoanalysis. But even years of psychoanalysis accomplished little, if anything, in curing premature ejaculation.

There is no evidence that men with premature ejaculation harbor unusual hostility toward women.

Low sexual desire alone is not equivalent to HSDD because of the requirement in HSDD that the low sexual desire causes marked distress and interpersonal difficulty and because of the requirement that the low desire is not better accounted for by another disorder in the DSM or by a general medical problem. It is therefore difficult to say exactly what causes HSDD. It is easier to describe, instead, some of the causes of low sexual desire.

In men, though there are theoretically more types of HSDD/low sexual desire, typically men are only diagnosed with one of three subtypes.

- Lifelong/generalised: The man has little or no desire for sexual stimulation (with a partner or alone) and never had.

- Acquired/generalised: The man previously had sexual interest in his present partner, but lacks interest in sexual activity, partnered or solitary.

- Acquired/situational: The man was previously sexually interested in his present partner but now lacks sexual interest in this partner but has desire for sexual stimulation (i.e. alone or with someone other than his present partner.)

Though it can sometimes be difficult to distinguish between these types, they do not necessarily have the same cause. The cause of lifelong/generalized HSDD is unknown. In the case of acquired/generalized low sexual desire, possible causes include various medical/health problems, psychiatric problems, low levels of testosterone or high levels of prolactin. One theory suggests that sexual desire is controlled by a balance between inhibitory and excitatory factors. This is thought to be expressed via neurotransmitters in selective brain areas. A decrease in sexual desire may therefore be due to an imbalance between neurotransmitters with excitatory activity like dopamine and norepinephrine and neurotransmitters with inhibitory activity, like serotonin. The, New York-based, "New View Campaign" organization has expressed skepticism about too much emphasis on explanations based on neurotransmitters because emphasis on such explanations have been made largely by "educational" efforts funded by Boehringer-Ingelheim while it was attempting to get the FDA to approve a drug affecting neurotransmitters for treatment for HSDD. Low sexual desire can also be a side effect of various medications. In the case of acquired/situational HSDD, possible causes include intimacy difficulty, relationship problems, sexual addiction, and chronic illness of the man’s partner. The evidence for these is somewhat in question. Some claimed causes of low sexual desire are based on empirical evidence. However, some are based merely on clinical observation. In many cases, the cause of HSDD is simply unknown.

There are some factors that are believed to be possible causes of HSDD in women. As with men, various medical problems, psychiatric problems (such as mood disorders), or increased amounts of prolactin can cause HSDD. Other hormones are believed to be involved as well. Additionally, factors such as relationship problems or stress are believed to be possible causes of reduced sexual desire in women. According to one recent study examining the affective responses and attentional capture of sexual stimuli in women with and without HSDD, women with HSDD do not appear to have a negative association to sexual stimuli, but rather a weaker positive association than women without HSDD

In the DSM-5, male hypoactive sexual desire disorder is characterized by "persistently or recurrently deficient (or absent) sexual/erotic thoughts or fantasies and desire for sexual activity", as judged by a clinician with consideration for the patient's age and cultural context. Female sexual interest/arousal disorder is defined as a "lack of, or significantly reduced, sexual interest/arousal", manifesting as at least three of the following symptoms: no or little interest in sexual activity, no or few sexual thoughts, no or few attempts to initiate sexual activity or respond to partner's initiation, no or little sexual pleasure/excitement in 75%-100% of sexual experiences, no or little sexual interest in internal or external erotic stimuli, and no or few genital/nongenital sensations in 75%-100% of sexual experiences.

For both diagnoses, symptoms must persist for at least six months, cause clinically significant distress, and not be better explained by another condition. Simply having lower desire than one's partner is not sufficient for a diagnosis. Self-identification of a lifelong lack of sexual desire as asexuality precludes diagnosis.

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.

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.

It is thought that people who suffer from this disorder, suffer from a dysfunction in the release of the chemical dopamine in the nucleus accumbens, the brain's primary reward center. This part of the brain is thought to play a role in pleasurable activities, including laughter, addiction, and music. Additionally, it is thought that depression, drug addiction, high levels of prolactin, low testosterone, and uses of certain medications might play a role in inhibiting dopamine. A spinal cord injury or chronic fatigue syndrome might also occasionally cause this disorder. Age may also be a cause of this disorder.

A sudden-onset sexual anhedonia can also be a symptom of sensory neuropathy, which is most commonly the result of pyridoxine toxicity (e.g., from large doses of vitamin B6 supplements).

In this case, the sexual dysfunction promptly resolves spontaneously once the B6 supplementation is stopped.

Increased serum prolactin (PRL) concentration in patients brains from psychiatric medicine can also affect sexuality.

Psychiatric medicine is known to cause the brain to form more dopamine receptors for the dopamine blocking effect. The normal amount of dopamine released during sex is insufficient to stimulate the larger number of dopamine receptors.

Dr. Mahmood Bhutta, an otorhinolaryngologist at John Radcliffe Hospital, states that sexually induced sneezing may be genetically determined, and may result from the way the central nervous system is wired:

"[T]his reflex demonstrates evolutionary relics in the wiring of a part of the nervous system called the autonomic nervous system. [...] This is the part beyond our control, and which controls things like our heart rate and the amount of light let in by our pupils. [...] Sometimes the signals in this system get crossed, and I think this may be why some people sneeze when they think about sex."

Another possible explanation concerns the existence of erectile tissue in the nose, which may become engorged during sexual arousal, triggering a sneeze.

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.

The person experiences sneezing as a result of sexual thoughts, arousal, intercourse, or orgasm. Sneezing occurs independent of external nasal stimuli or allergens, and may occur at any point during a sexual experience. Both men and women are affected by the phenomenon.

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).

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.

Normally, a human being is able to feel pleasure from an orgasm. Upon reaching a climax, chemicals are released in the brain and motor signals are activated that will cause quick cycles of muscle contraction in the corresponding areas of both males and females. Sometimes, these signals can cause other involuntary muscle contractions such as body movements and vocalization. Finally, during orgasm, upward neural signals go to the cerebral cortex and feelings of intense pleasure are experienced. People who have this disorder are aware of reaching an orgasm, as they can feel the physical effects of it, but they experience very limited or no sort of pleasure.

Phallophobia in its narrower sense is a fear of the erect penis and in a broader sense an excessive aversion to masculinity.

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.

If a couple is experiencing infertility as a result of retrograde ejaculation and medications are not helping, the male's ejaculate may be centrifuged and the isolated sperm injected directly into the woman through the use of intrauterine insemination. In more severe cases, in-vitro fertilization with intracytoplasmic sperm injection may be used.

Sigmund Freud has footnoted the possibility that this fear may be derived from a lack of ingenuity allowing one to ornamentally distance the copulatory organs from the excretory organs. Such a condition can affect both men and women. For others, symptoms include what characterizes a panic attack. It does not necessarily have to be induced by an uncovered penis, but may also result from seeing the manbulging outline or curvature of the penis, perhaps through clothes consisting of thin fabric. In more extreme cases it has been likened to the fight or flight response ingrained within the human body wherein an individual ceases to be intimate with their male partner and is unable to visit mixed gender establishments where people are likely to wear more revealing clothing, such as a gym, beach, cinema or livingrooms with a switched on monitor. The fear can recur through any of the senses including accidental touch, sight, hearing the word penis or thinking about an erection. The phobia may have developed from a condition such as dyspareunia, a trauma (usually sexual) that occurred during childhood, but can also have a fortuitous origin. In literature covering human sexuality, it is used as an adjective only to negatively allude to penetrative sex acts. Men who have the phobia may try to avoid wearing jeans and other light fabrics, especially in public. Some analysts have purported that the condition may be inherited or may be a combination of genetic inheritance and life experiences. For men with the condition, one of the byproducts is difficulty consummating with a partner due to a sense of vulnerability. This vulnerability may have developed during childhood because they grew up being told by their parents that sex and its physiological functions were evil, sinful and dirty, but were subsequently unable to detach such shameful feelings nor reverse it upon reaching adulthood, even when romantic initiatives were subsequently approved of or encouraged by their parents.

According to one hypothesis, "POIS is caused by Type-I and Type-IV allergy to the males' own semen". Specifically,

POIS could also be caused by an auto-immune reaction not to semen itself, but to another substance that is released during ejaculation, such as to cytokines.

The allergy hypothesis has been disputed. According to one study, "IgE-mediated semen allergy in men may not be the potential mechanism of POIS".