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.

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

A number of studies have explored the factors that contribute to female sexual arousal disorder and female orgasmic disorder. These factors include both psychological and physical factors. Psychologically, possible causes of the disorder include the impact of childhood and adolescence experiences and current events – both within the individual and within the current relationship.

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.

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.

There has been little investigation of the impact of individual factors on female sexual dysfunction. Such factors include stress, levels of fatigue, gender identity, health, and other individual attributes and experiences, such as dysfunctional sexual beliefs that may affect sexual desire or response. Over exposure to pornography-style media is also thought to lead to poor body image, self-consciousness and lowered self-esteem. An individual's sexual activity is disrupted by overwhelming emotional distress resulting in inability to attain sexual pleasure. Sexual dysfunction can also occur secondary to major psychiatric disorders, including depression.

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

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.

Surgical intervention for a number of conditions may remove anatomical structures necessary to erection, damage nerves, or impair blood supply. Erectile dysfunction is a common complication of treatments for prostate cancer, including prostatectomy and destruction of the prostate by external beam radiation, although the prostate gland itself is not necessary to achieve an erection. As far as inguinal hernia surgery is concerned, in most cases, and in the absence of postoperative complications, the operative repair can lead to a recovery of the sexual life of patients with preoperative sexual dysfunction, while, in most cases, it does not affect patients with a preoperative normal sexual life.

ED can also be associated with bicycling due to both neurological and vascular problems due to compression. The increase risk appears to be about 1.7-fold.

Concerns that use of pornography can cause erectile dysfunction have not been substantiated in epidemiological studies according to a recent literature review. However, another review and case studies article maintains that use of pornography does indeed cause erectile dysfunction, and critiques the previously described literature review.

Erectile dysfunction is characterized by the regular or repeated inability to obtain or maintain an erection.

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.

Sexual maturation disorder is a disorder of anxiety or depression related to an uncertainty about one's gender identity or sexual orientation. The World Health Organization (WHO) lists sexual maturation disorder in the ICD-10, under "Psychological and behavioural disorders associated with sexual development and orientation".

Sexual orientation, by itself, is not a disorder and is not classified under this heading. It differs from ego-dystonic sexual orientation where the sexual orientation or gender identity is repressed or denied.

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.

As the disorder progresses in life, it can increase in severity, and cause other behaviors or actions in late adolescence and adulthood. “A strong and persistent cross-gender identification in adolescents and adults [can cause a] disturbance manifested by symptoms such as a stated desire to be the other sex, frequent passing as the other sex, desire to live or be treated as the other sex, or the conviction that he or she has the typical feelings and reactions of the other sex” (APA, 2000). This can cause severe conflict for the individual living in a society which endorses and enforces adherence to strict gender roles. In a more persistent disassociation with one’s own body or gender, someone can go to more extreme lengths to feel as though they are fulfilled or satisfied with themselves. This can lead these individuals to engage in behavior that displaces their emotions. These individuals may also seek to undergo sex reassignment surgery. “Persistent discomfort with his or her sex or sense of inappropriateness in the gender role of that sex in adolescents and adults [can cause a] disturbance manifested by symptoms such as preoccupation with getting rid of primary and secondary sex characteristics (e.g., request for hormones, surgery, or other procedures to physically alter sexual characteristics to simulate the other sex) or belief that he or she was born the wrong sex” (APA, 2000).

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).

Hypersexuality may negatively impact an individual. The concept of hypersexuality as an addiction was started in the 1970s by former members of Alcoholics Anonymous who felt they experienced a similar lack of control and compulsivity with sexual behaviors as with alcohol. Multiple 12-step style self-help groups now exist for people who identify as sex addicts, including Sex Addicts Anonymous, Sexaholics Anonymous, Sex and Love Addicts Anonymous, and Sexual Compulsives Anonymous. Some hypersexuals may treat their condition with the usage of medication or any foods considered to be anaphrodisiacs. Other hypersexuals may choose a route of consultation, such as psychotherapy, self-help groups or counselling.

As a paraphilia, breast fetishism (also known as mastofact, breast partialism, or mazophilia) is a highly atypical sexual interest focused on female breasts (see partialism). The term "breast fetishism" is also used in the non-paraphilic sense, to refer to cultural attention to female breasts and the sexuality they represent, with debate existing as to whether the modern widespread fascination with breasts among heterosexual males in western societies is a sexual fetish.

, a proposal to add "Sexual Addiction" to the Diagnostic and Statistical Manual of Mental Disorders (DSM) system has failed to get support of the American Psychiatric Association (APA). The DSM does include an entry called Sexual Disorder Not Otherwise Specified (Sexual Disorder NOS) to apply to, among other conditions, "distress about a pattern of repeated sexual relationships involving a succession of lovers who are experienced by the individual only as things to be used".

The International Statistical Classification of Diseases and Related Health Problems (ICD-10) of the World Health Organization (WHO), includes two relevant entries. One is "Excessive Sexual Drive" (coded F52.7), which is divided into satyriasis for males and nymphomania for females. The other is "Excessive Masturbation" or "Onanism (excessive)" (coded F98.8).

Some authors have questioned whether it makes sense to discuss hypersexuality at all, arguing that labeling sexual urges "extreme" merely stigmatizes people who do not conform to the norms of their culture or peer group.

Links between maternal smoking and TDS are tenuous, but there are stronger associations between maternal alcohol consumption and incidences of cryptorchidism in sons. Smoking does however affect the growth of a fetus, and low birth weight is shown to increase the likelihood of all the disorders encompassed by TDS. Maternal obesity, resulting in gestational diabetes, has also been shown to be a risk factor for impaired testes development and TDS symptoms in sons.

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.

A case report of male breast cancer subsequent to bicalutamide-induced gynecomastia has been published. According to the authors, "this is the second confirmed case of breast cancer in association with bicalutamide-induced gynaecomastia (correspondence AstraZeneca)." It is notable, however, that gynecomastia does not seem to increase the risk of breast cancer in men. Moreover, the lifetime incidence of breast cancer in men is approximately 0.1%, the average age of diagnosis of prostate cancer and male breast cancer are similar (around 70 years), and millions of men have been treated with bicalutamide for prostate cancer, all of which are potentially in support of the notion of chance co-occurrences. In accordance, the authors concluded that "causality cannot be established" and that it was "probable that the association is entirely coincidental and sporadic."

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.

Underwear fetishism is a sexual fetishism relating to undergarments, and refers to preoccupation with the sexual excitement of certain types of underwear, including panties, stockings, pantyhose, bras, or other items. Some people experience sexual excitement from wearing, while others get their excitement when observing or handling the underwear worn by another, or watching somebody putting underwear on/taking it off. Some may steal used underwear to get satisfaction. Not only does this include physical contact with the garment(s), or their wearers, but also includes arousal by printed or electronic image with depictions of underwear.

Underwear fetishism is not considered as paraphilia unless it causes distress or serious problems for the person or those associated with them.

Because bicalutamide blocks the , like all antiandrogens, it can interfere with the androgen-mediated sexual differentiation of the genitalia (and brain) during prenatal development. In pregnant rats given bicalutamide at a dosage of 10 mg/kg/day (resulting in circulating drug levels approximately equivalent to two-thirds of human therapeutic concentrations) and above, feminization of male offspring, such as reduced anogenital distance and hypospadias, as well as impotence, were observed. No other teratogenic effects were observed in rats or rabbits receiving up to very high dosages of bicalutamide (that corresponded to up to approximately two times human therapeutic levels), and no teratogenic effects of any sort were observed in female rat offspring at any dosage. As such, bicalutamide is a selective reproductive teratogen in males, and may have the potential to produce undervirilization/sexually ambiguous genitalia in male fetuses.