Around 15% of all adult males, up to 35% of men who are evaluated for male infertility, and around 80% of men who are infertile due to some other cause, have varicocele.

A hydrocele testis is not generally thought to affect fertility. However, it may be indicative of other factors that may affect fertility.

Often the greatest concern with respect to varicocele is its effect on male fertility. The relationship between varicocele and infertility is unclear; some men with the condition are fertile, some have sperm that are normal in shape and move normally, but are compromised in function, and some have sperm with abnormal shapes or that do not move well. Theories as to how variocele affects sperm function include damage via excess heat caused by the blood pooling and oxidative stress on sperm (ROS).

Tobacco smoking and mutations in the gene expressing glutathione S-transferase Mu 1 both put men at risk for infertility; these factors may also exacerbate the risk that varicocele will affect fertility.

Torsion is due to a mechanical twisting process. It is also believed that torsion occurring during fetal development can lead to so-called neonatal torsion or vanishing testis, and is one of the causes of an infant being born with monorchism (one testicle).

A hydrocele testis is an accumulation of clear fluid in the tunica vaginalis, the most internal of membranes containing a testicle. A primary hydrocele causes a painless enlargement in the scrotum on the affected side and is thought to be due to the defective absorption of fluid secreted between the two layers of the tunica vaginalis (investing membrane). A secondary hydrocele is secondary to either inflammation or a neoplasm in the testis.

A hydrocele usually occurs on one side, but can also affect both sides. The accumulation can be a marker of physical trauma, infection, tumor or varicocele surgery, but the cause is generally unknown. Indirect inguinal hernia indicates increased risk of hydrocele.

A hydrocele is normally seen in infant boys, as an enlarged scrotum. In infant girls, it appears as enlarged labia. However, hydroceles are more common in boys than girls.

Torsion is most frequent among adolescents with about 65% of cases presenting between 12–18 years of age. It occurs in about 1 in 4,000 to 1 per 25,000 males per year before 25 years of age; but it can occur at any age, including infancy.

Secondary hydroceles due to testicular diseases can be the result of cancer, trauma (such as a hernia), or orchitis (inflammation of testis), and can also occur in infants undergoing peritoneal dialysis. A hydrocele is not a cancer but it should be excluded clinically if a presence of a testicular tumor is suspected, however, there are no publications in the world literature that report a hydrocele in association with testicular cancer. Secondary hydrocele is most frequently associated with acute or chronic epididymo-orchitis. It is also seen with torsion of the testis and with some testicular tumors. A secondary hydrocele is usually lax and of moderate size: the underlying testis is palpable. A secondary hydrocele subsides when the primary lesion resolves.

- Acute/chronic epididymo-orchitis

- Torsion of testis

- Testicular tumor

- Hematocele

- Filarial hydrocele

- Post herniorrhaphy

- Hydrocele of an hernial sac

A hydrocele can be produced in four ways:

- by excessive production of fluid within the sac, e.g. secondary hydrocele

- through defective absorption of fluid

- by interference with lymphatic drainage of scrotal structures as in case of elephantiasis

- by connection with a hernia of the peritoneal cavity in the congenital variety, which presents as hydrocele of the cord

Spermatoceles can originate as diverticulum from the tubules found in the head of the epididymis. Sperm formation gradually causes the diverticulum to increase in size, causing a spermatocele. They are due to continuity between the epididymis and tunica vaginalis.

They are also believed to result from epididymitis, physical trauma, or vasectomy. Scarring of any part of the epididymis can cause it to become obstructed and in turn form a spermatocele.

90% of ruptured testes are successfully repaired when treated surgically within 72 hours; the percentage of successful treatment drops to 45% after this period. Though not typically fatal, testicular rupture can cause hypogonadism, low self-esteem, and infertility.

A ectopic testis is a testicle that, although not an undescended testicle, has taken a non-standard path through the body and ended up in an unusual location.

The positions of the ectopic testis may be: in the lower part of the abdomen, front of thigh, femoral canal, skin of penis or behind the scrotum. The testis is usually developed, and accompanied by an indirect inguinal hernia. It may be divorced from the epididymis which may lie in the scrotum.

Most cases of polyorchidism are asymptomatic, and are discovered incidentally, in the course of treating another condition. In the majority of cases, the supernumerary testicle is found in the scrotum.

However, polyorchidism can occur in conjunction with cryptorchidism, where the supernumerary testicle is undescended or found elsewhere in the body. These cases are associated with a significant increase in the incidence of testicular cancer: 0.004% for the general population vs 5.7% for a supernumerary testicle not found in the scrotum.

Polyorchidism can also occur in conjunction with infertility, inguinal hernia, testicular torsion, epididymitis, hydrocele testis and varicocele. However, it is not clear whether polyorchidism causes or aggravates these conditions, or whether the existence of these conditions leads sufferers to seek medical attention and thus become diagnosed with a previously undetected supernumerary testicle.

Spermatocele () is a retention cyst of a tubule of the rete testis or the head of the epididymis distended with barely watery fluid that contains spermatozoa. Small spermatoceles are relatively common, occurring in an estimated 30 percent of all men. They vary in size from several millimeters to many centimeters. Spermatoceles are generally not painful. However, some men may experience discomfort from larger spermatoceles. They are not cancerous, nor do they cause an increased risk of testicular cancer. Additionally, unlike varicoceles, they do not have a negative impact on fertility.

Fournier's gangrene ( an aggressive and rapidly spreading infection of the perineum ) usually presents with fever and intense pain. It is a rare condition but fatal if not identified and aggressively treated with a combination of surgical debridement and broad spectrum antibiotics.

Chronic scrotal pain (pain for greater than 3 months) may occur due to a number of underlying conditions. It occurs in 15-19% of people post vasectomy, due to infections such as epididymitis, prostatitis, and orchitis, as well as varicocele, hydrocele, spermatocele, polyarteritis nodosa, testicular torsion, previous surgery and trauma. In 25% of cases the cause is never determined. The pain can persist for a long and indefinite period of time following the vasectomy, in which case it is termed post-vasectomy pain syndrome (PVPS).

Polyorchidism is the incidence of more than two testicles. It is a very rare congenital disorder, with fewer than 201 cases reported in medical literature and 6 cases (two horses, two dogs and two cats) in veterinary literature.

Polyorchidism is generally diagnosed via an ultrasound examination of the testicles. However, the diagnosis of polyorchidism should include histological confirmation. The most common form is triorchidism, or tritestes, where three testicles are present. The condition is usually asymptomatic. A man who has polyorchidism is known as a polyorchid.

A potential testicular rupture should be evaluated with ultrasound imaging. Testicular rupture is treated with surgery, though the procedure performed depends on the magnitude of the injury and the salvageability of the tissue. An orchiectomy - removal of the affected testis - is done when the testis is not salvageable and leads to reduced semen quality and higher rates of endocrine dysfunction than repair of salvageable tissue.

In most full-term infant boys with cryptorchidism but no other genital abnormalities, a cause cannot be found, making this a common, sporadic, unexplained (idiopathic) birth defect. A combination of genetics, maternal health, and other environmental factors may disrupt the hormones and physical changes that influence the development of the testicles.

- Severely premature infants can be born before descent of testes. Low birth weight is also a known factor.

- A contributing role of environmental chemicals called endocrine disruptors that interfere with normal fetal hormone balance has been proposed. The Mayo Clinic lists "parents' exposure to some pesticides" as a known risk factor.

- Diabetes and obesity in the mother.

- Risk factors may include exposure to regular alcohol consumption during pregnancy (5 or more drinks per week, associated with a 3x increase in cryptorchidism, when compared to non-drinking mothers. Cigarette smoking is also a known risk factor.

- Family history of undescended testicle or other problems of genital development.

- Cryptorchidism occurs at a much higher rate in a large number of congenital malformation syndromes. Among the more common are Down syndrome Prader–Willi syndrome, and Noonan syndrome.

- In vitro fertilization, use of cosmetics by the mother, and preeclampsia have also been recognized as risk factors for development of cryptorchidism.

In 2008 a study was published that investigated the possible relationship between cryptorchidism and prenatal exposure to a chemical called phthalate (DEHP) which is used in the manufacture of plastics. The researchers found a significant association between higher levels of DEHP metabolites in the pregnant mothers and several sex-related changes, including incomplete descent of the testes in their sons. According to the lead author of the study, a national survey found that 25% of U.S. women had phthalate levels similar to the levels that were found to be associated with sexual abnormalities.

A 2010 study published in the European medical journal "Human Reproduction" examined the prevalence of congenital cryptorchidism among offspring whose mothers had taken mild analgesics, primarily over-the-counter pain medications including ibuprofen (e.g. Advil) and paracetamol (acetaminophen). Combining the results from a survey of pregnant women prior to their due date in correlation with the health of their children and an "ex vivo" rat model, the study found that pregnant women who had been exposed to mild analgesics had a higher prevalence of baby boys born with congenital cryptorchidism.

New insight into the testicular descent mechanism has been hypothesized by the concept of a male programming window (MPW) derived from animal studies. According to this concept, testicular descent status is "set" during the period from 8 to 14 weeks of gestation in humans. Undescended testis is a result of disruption in androgen levels only during this programming window.

This can be due to:

- One testicle not descending into the scrotum during normal embryonic or fetal development (3–4% of 'normal' live births), also known as undescended testis or cryptorchidism. In this case the testis is within the abdominal cavity, somewhere along the normal route of descent – most commonly, within the inguinal canal. Such a testis has an increased risk of malignancy.

- One testicle may disappear during development (the so-called vanishing testis) due to some intrauterine insult. This is thought to be most likely vascular, such as testicular torsion.

- One testicle may have been surgically removed through orchiectomy.

- One testicle may be injured.

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.

A testicular nubbin is the residual tissue of the human testis after a supposed perinatal vascular accident involving the testicular blood supply. The blood supply of the testis twists (called torsion) thereby cutting off the blood supply to the testis and results in testicular atrophy (shrinking). The nubbin is usually identified in childhood by the absence of a palpable testis in the scrotal sac. The tissue remnant usually includes fibrous tissue and signs of old infarction with hemosiderin deposition identified histologically. There is some disagreement as to whether these should be removed and whether there is a risk of future malignancy. They are typically removed surgically by pediatric urologists or pediatric general surgeons through either a scrotal or inguinal (or both) incision.

One of the strongest arguments for early orchiopexy is reducing the risk of testicular cancer. About 1 in 500 men born with one or both testes undescended develops testicular cancer, roughly a 4 to 40 fold increased risk. The peak incidence occurs in the 3rd and 4th decades of life. The risk is higher for intra-abdominal testes and somewhat lower for inguinal testes, but even the "normally descended" testis of a man whose other testis was undescended has about a 20% higher cancer risk than those of other men.

The most common type of testicular cancer occurring in undescended testes is seminoma. It is usually treatable if caught early, so urologists often recommend that boys who had orchiopexy as infants be taught testicular self-examination, to recognize testicular masses and seek early medical care for them. Cancer developing in an intra-abdominal testis would be unlikely to be recognized before considerable growth and spread, and one of the advantages of orchiopexy is that a mass developing in a scrotal testis is far easier to recognize than an intra-abdominal mass.

It was originally felt that orchidopexy resulted in easier detection of testis cancer but did not lower the risk of actually developing cancer. However, recent data has resulted in a paradigm shift. The New England Journal of Medicine published in 2007 that orchidopexy performed before puberty resulted in a significantly reduced risk of testicular cancer than if done after puberty.

The risk of malignancy in the undescended testis is 4 to 10 times higher than that in the general population and is approximately 1 in 80 with a unilateral undescended testis and 1 in 40 to 1 in 50 for bilateral undescended testes. The peak age for this tumor is 15–45 yr. The most common tumor developing in an undescended testis is a seminoma (65%); in contrast, after orchiopexy, seminomas represent only 30% of testis tumors.

Although extremely rare, monorchism has been observed to be characteristic of some animal species, notably in beetles.

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".

Though urinary tract infections in men are rare, bacterial infection is the most common cause of acute epididymitis. The bacteria in the urethra back-track through the urinary and reproductive structures to the epididymis. In rare circumstances, the infection reaches the epididymis via the bloodstream.

In sexually active men, "Chlamydia trachomatis" is responsible for two-thirds of acute cases, followed by "Neisseria gonorrhoeae" and "E. coli" (or other bacteria that cause urinary tract infection). Particularly among men over age 35 in whom the cause is "E. coli", epididymitis is commonly due to urinary tract obstruction. Less common microbes include "Ureaplasma", Mycobacterium, and "cytomegalovirus", or "Cryptococcus" in patients with HIV infection. "E. coli" is more common in boys before puberty, the elderly, and men who have sex with men. In the majority of cases in which bacteria are the cause, only one side of the scrotum or the other is the locus of pain.

Non-infectious causes are also possible. Reflux of sterile urine (urine without bacteria) through the ejaculatory ducts may cause inflammation with obstruction. In children, it may be a response following an infection with enterovirus, adenovirus or "Mycoplasma pneumoniae". Rare non-infectious causes of chronic epididymitis include sarcoidosis (more prevalent in black men) and Behçet's disease.

Any form of epididymitis can be caused by genito-urinary surgery, including prostatectomy and urinary catheterization. Congestive epididymitis is a long-term complication of vasectomy. Chemical epididymitis may also result from drugs such as amiodarone.