The history should include prior testicular or penile insults (torsion, cryptorchidism, trauma), infections (mumps orchitis, epididymitis), environmental factors, excessive heat, radiation, medications, and drug use (anabolic steroids, alcohol, smoking).

Sexual habits, frequency and timing of intercourse, use of lubricants, and each partner's previous fertility experiences are important.

Loss of libido and headaches or visual disturbances may indicate a pituitary tumor.

The past medical or surgical history may reveal thyroid or liver disease (abnormalities of spermatogenesis), diabetic neuropathy (retrograde ejaculation), radical pelvic or retroperitoneal surgery (absent seminal emission secondary to sympathetic nerve injury), or hernia repair (damage to the vas deferens or testicular blood supply).

A family history may reveal genetic problems.

The diagnosis of infertility begins with a medical history and physical exam by a physician, physician assistant, or nurse practitioner. Typically two separate semen analyses will be required. The provider may order blood tests to look for hormone imbalances, medical conditions, or genetic issues.

Examples of functional problems of the reproductive system include:

- Impotence - The inability of a male to produce or maintain an erection.

- Hypogonadism - A lack of function of the gonads, in regards to either hormones or gamete production.

- Ectopic pregnancy - When a fertilized ovum is implanted in any tissue other than the uterine wall.

- Hypoactive sexual desire disorder - A low level of sexual desire and interest.

- Female sexual arousal disorder - A condition of decreased, insufficient, or absent lubrication in females during sexual activity

- Premature ejaculation - A lack of voluntary control over ejaculation.

- Dysmenorrhea - Is a medical condition of pain during menstruation that interferes with daily activities

Males with penile agenesis but normal testes are of otherwise normal male appearance.

Males with testicular agenesis tend not to produce the reproductive hormone 5aDHT at any stage of their lives. As a result, they tend toward prepubescent appearance, with infantile skin texture, developing little body hair particularly in the crotch area, even vellus hair. Without genitalia of either sex, the perineum is therefore left smooth. Also muscular development is retarded and testicular agenetics are of rather frail build with short limbs and small hands and feet.

However certain male features are results of other male gender-marker hormones, "androgens", which develop male secondary sex characteristics, among which features are the deepening of the voice and facial hair.

A reproductive system disease is any disease of the reproductive system.

Female infertility refers to infertility in female humans. It affects an estimated 48 million women with the highest prevalence of infertility affecting people in South Asia, Sub-Saharan Africa, North Africa/Middle East, and Central/Eastern Europe and Central Asia. Infertility is caused by many sources, including nutrition, diseases, and other malformations of the uterus. Infertility affects women from around the world, and the cultural and social stigma surrounding it varies.

Hypospadias presents as an abnormal location for the end of the urethra which is typically found on the distal end of the penis. It is generally diagnosed at birth from visual confirmation of the hallmark features. As well as an unusual location of the urethra, the prepuce (foreskin) is typically incomplete as well. The abnormal ‘hooded’ prepuce is what often draws attention to the condition but can occur separately to hypospadias.

The symptoms of Leydig cell hypoplasia include pseudohermaphroditism (i.e., feminized, ambiguous, or relatively mildly underdeveloped (e.g., micropenis, severe hypospadias, and/or cryptorchidism (undescended testes)) external genitalia), a female gender identity or gender variance, hypergonadotropic hypogonadism (hypogonadism despite high levels of gonadotropins), delayed, impaired, or fully absent puberty with an associated reduction in or complete lack of development of secondary sexual characteristics (sexual infantilism), impaired fertility or complete sterility, tall stature (due to delayed epiphyseal closure), eunuchoid skeletal proportions, delayed or absent bone maturation, and osteoporosis.

Penile agenesis is a birth defect in humans, occurring about once in 5–6 million male births, in which a male child is born without a penis.

A partner condition is testicular or gonadal agenesis. This is when a male child is born without gonads and consequently develops no testes. Penile agenesis occurs often as a consequence of Testicular agenesis, but the reverse is never the case. Most patients in both cases have no known family history and usually have an otherwise normal male anatomy.

A male genital disease is a condition that affects the male reproductive system. An example is orchitis.

non infection disease

In Cryptorchidism a diagnosis is made from a physical examination which is performed when the baby is lacking one or both testes in the dependant portion of the scrotal sac. 70% of cryptorchid testes can be felt and are unable to be pulled into the scrotum or retreats quickly after being pulled into a higher position. In 30% of cases the testes cannot be felt indicating an intra-abdominal location. The risk factors for Cryptorchidism are:

- A family history of the condition

- Low birth weight

- Prematurity

Disorders of sex development (DSD), sometimes referred to as disorders of sex differentiation or differences of sex development, are medical conditions involving the reproductive system. More specifically, these terms refer to "congenital conditions in which development of chromosomal, gonadal, or anatomical sex is atypical."

The term has been controversial, and research has shown that affected people experience a negative impact, with the terminology impacting choice and utilization of health care providers. The World Health Organization and many medical journals still reference DSDs as intersex traits or conditions. The Council of Europe, and Inter-American Commission on Human Rights have called for a review of medical classifications that unnecessarily medicalize intersex traits.

Infertility is the inability of a person, animal or plant to reproduce by natural means. It is usually not the natural state of a healthy adult, except notably among certain eusocial species (mostly haplodiploid insects).

In humans, infertility is the inability to become pregnant or carry a pregnancy to full term. There are many causes of infertility, including some that medical intervention can treat. Estimates from 1997 suggest that worldwide about five percent of all hetersexual couples have an unresolved problem with infertility. Many more couples, however, experience involuntary childlessness for at least one year: estimates range from 12% to 28%." 20-30% of infertility cases are due to male infertility, 20-35% are due to female infertility, and 25-40% are due to combined problems in both parts. In 10-20% of cases, no cause is found. The most common cause of female infertility is ovulatory problems which generally manifest themselves by sparse or absent menstrual periods. Male infertility is most commonly due to deficiencies in the semen, and semen quality is used as a surrogate measure of male fecundity.

Women who are fertile experience a natural period of fertility before and during ovulation, and they are naturally infertile for the rest of the menstrual cycle. Fertility awareness methods are used to discern when these changes occur by tracking changes in cervical mucus or basal body temperature.

The condition may be due to:

- Turner syndrome, and its variations (i.e. mosaicism)

- XX gonadal dysgenesis, also pure gonadal dysgenesis, 46,XX

- Swyer syndrome, also pure gonadal dysgenesis, 46,XY

- Perrault syndrome, XX gonadal dysgenesis + sensorineural hearing loss

- Mixed gonadal dysgenesis

- Exposure to environmental endocrine disruptors

Leydig cell hypoplasia (or aplasia) (LCH), also known as Leydig cell agenesis, is a rare autosomal recessive genetic and endocrine syndrome affecting an estimated 1 in 1,000,000 genetic males. It is characterized by an inability of the body to respond to luteinizing hormone (LH), a gonadotropin which is normally responsible for signaling Leydig cells of the testicles to produce testosterone and other androgen sex hormones. The condition manifests itself as pseudohermaphroditism (partially or fully underdeveloped genitalia), hypergonadotropic hypogonadism (decreased or lack of production of sex steroids by the gonads despite high circulating levels of gonadotropins), reduced or absent puberty (lack of development of secondary sexual characteristics, resulting in sexual infantilism if left untreated), and infertility.

Leydig cell hypoplasia does not occur in biological females as they do not have either Leydig cells or testicles. However, the cause of the condition in males, luteinizing hormone insensitivity, does affect females, and because LH plays a role in the female reproductive system, it can result in primary amenorrhea or oligomenorrhea (absent or reduced menstruation), infertility due to anovulation, and ovarian cysts.

A related condition is follicle-stimulating hormone (FSH) insensitivity, which presents with similar symptoms to those of Leydig cell hypoplasia but with the symptoms in the respective sexes reversed (i.e., hypogonadism and sexual infantilism in females and merely problems with fertility in males). Despite their similar causes, FSH insensitivity is considerably less common in comparison to LH insensitivity.

Gonadal dysgenesis is any congenital developmental disorder of the reproductive system characterized by a progressive loss of germ cells on the developing gonads of an embryo. This loss leads to extremely hypoplastic (underdeveloped) and dysfunctioning gonads mainly composed of fibrous tissue, hence the name streak gonads—i.e., a form of aplasia in which the ovary is replaced by functionless tissue. The accompanying hormonal failure also prevents the development of secondary sex characteristics in either sex, resulting in a sexually infantile female appearance and infertility.

The first type of gonadal dysgenesis discovered was Turner syndrome.

Anorchia (or anorchism) is an XY disorder of sex development in which individuals have both testes absent at birth. Within a few weeks of fertilization, the embryo develops rudimentary gonads (testes), which produce hormones responsible for the development of the reproductive system. If the testes fail to develop within eight weeks, the baby will develop female genitalia (see Swyer syndrome). If the testes begin to develop but are lost or cease to function between eight and 10 weeks, the baby will have ambiguous genitalia when it is born. However, if the testes are lost after 14 weeks, the baby will have partial male genitalia with the notable absence of gonads.

Tests include observable lack of testes, low testosterone levels (typical female levels), elevated follicle stimulating hormone and luteinizing hormone levels, XY karyotype, ultrasound or magnetic resonance imaging showing absent gonadal tissue, low bone density, low anti-Müllerian hormone levels, and surgical exploration for evidence of male gonadal tissue.

Alternatively, female genital diseases can be more strictly classified by location of the disease, which, in turn, can be broadly divided between diseases that affect the female internal genitalia and those that affect the female external genitalia.

A female genital disease is a condition that affects the female reproductive system.

Because both the Wolffian ducts and Müllerian ducts begin to develop, the tissues are often intertwined, resulting in obstruction or nonpatency of the vas deferens or other parts of the reproductive excretory ducts. This can result in infertility, the most serious potential problem caused by this condition. Sometimes, transverse testicular ectopia is evident.

Cryptorchidism in AMH deficiency suggests that AMH may play a role in transabdominal testicular descent, perhaps by facilitating contraction of the gubernaculum.

Other Müllerian derivatives which may be present in at least a rudimentary form are the cervix, upper part of the vagina, and fallopian tubes.

The condition can come to attention because of a bulge in the inguinal canal of an XY infant due to herniation of the uterus. The presence of a uterus may be noticed if an ultrasound or MRI of the pelvis is performed to locate the testes or for other reasons. Occasionally the uterus is discovered during abdominal surgery for some other purpose in later childhood or adult life.

Although persistent Müllerian duct syndrome is classified as an intersex condition, it does not involve ambiguity or malformation of the external genitalia, which appear typical (apart from cryptorchidism if present). Sometimes the uterus enters a hernia. Sometimes the Müllerian structures get entangled with the spermatic ducts and interfere with the descent of the testes.

Apart from humans, this syndrome has been reported in dogs.

Women with hypogonadism do not begin menstruating and it may affect their height and breast development. Onset in women after puberty causes cessation of menstruation, lowered libido, loss of body hair and hot flashes. In boys it causes impaired muscle and beard development and reduced height. In men it can cause reduced body hair and beard, enlarged breasts, loss of muscle, and sexual difficulties. A brain tumor (central hypogonadism) may involve headaches, impaired vision, milky discharge from the breast and symptoms caused by other hormone problems.

There is no unanimous definition of female infertility, because the definition depends on social and physical characteristics which may vary by culture and situation. NICE guidelines state that: "A woman of reproductive age who has not conceived after 1 year of unprotected vaginal sexual intercourse, in the absence of any known cause of infertility, should be offered further clinical assessment and investigation along with her partner." It is recommended that a consultation with a fertility specialist should be made earlier if the woman is aged 36 years or over, or there is a known clinical cause of infertility or a history of predisposing factors for infertility. According to the World Health Organization (WHO), infertility can be described as the inability to become pregnant, maintain a pregnancy, or carry a pregnancy to live birth.

A clinical definition of infertility by the WHO and ICMART is “a disease of the reproductive system defined by the failure to achieve a clinical pregnancy after 12 months or more of regular unprotected sexual intercourse.” Infertility can further be broken down into primary and secondary infertility. Primary infertility refers to the inability to give birth either because of not being able to become pregnant, or carry a child to live birth, which may include miscarriage or a stillborn child.

Swyer syndrome represents one phenotypic result of a failure of the gonads to develop properly, and hence is part of a class of conditions termed gonadal dysgenesis. There are many forms of gonadal dysgenesis.

Swyer syndrome is an example of a condition in which an externally unambiguous female body carries dysgenetic, atypical, or abnormal gonads. Other examples include complete androgen insensitivity syndrome, partial X chromosome deletions, lipoid congenital adrenal hyperplasia, and Turner syndrome.

A freemartin or free-martin (sometimes martin heifer) is an infertile female mammal with masculinized behavior and non-functioning ovaries. Genetically the animal is chimeric: Karyotyping of a sample of cells shows XX/XY chromosomes. The animal originates as a female (XX), but acquires the male (XY) component in utero by exchange of some cellular material from a male twin, via vascular connections between placentas: an example of microchimerism. Externally, the animal appears female, but various aspects of female reproductive development are altered due to acquisition of anti-Müllerian hormone from the male twin. Freemartinism is the normal outcome of mixed-sex twins in all cattle species that have been studied, and it also occurs occasionally in other mammals including sheep, goats and pigs.

Hypogonadism can involve just hormone production or just fertility, but most commonly involves both.

- Examples of hypogonadism that affect hormone production more than fertility are hypopituitarism and Kallmann syndrome; in both cases, fertility is reduced until hormones are replaced but can be achieved solely with hormone replacement.

- Examples of hypogonadism that affect fertility more than hormone production are Klinefelter syndrome and Kartagener syndrome.