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".

Treatment depends on the proximate cause. In one study, it was reported that 9 of 13 men who underwent vasectomy reversal in an attempt to relieve post-vasectomy pain syndrome became pain-free, though the followup was only one month in some cases. Another study found that 24 of 32 men had relief after vasectomy reversal.

Nerve entrapment is treated with surgery to free the nerve from the scar tissue, or to cut the nerve. One study reported that denervation of the spermatic cord provided complete relief at the first follow-up visit in 13 of 17 cases, and that the other four patients reported improvement. As nerves may regrow, long-term studies are needed.

One study found that epididymectomy provided relief for 50% of patients with post-vasectomy pain syndrome.

Orchiectomy is recommended usually only after other surgeries have failed.

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).

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.

Treatment is often with NSAIDs and antibiotics however, this is not always effective.

These headaches are estimated to appear in roughly 1% of the population. They can occur with sexual activity at any age. It is more common in men than women, with studies putting the gender ratio between 1.2:1 and 3:1.

Orchialgia is long-term pain of the testes. It is considered chronic if it has persisted for more than 3 months. Orchialgia may be caused by injury, infection, surgery, cancer or testicular torsion and is a possible complication after vasectomy. IgG4-related disease is a more recently identified cause of chronic orchialgia.

One author describes the syndromes of chronic testicular pain thus:"The complaint is of a squeezing deep ache in the testis like the day after you got kicked there, often bilateral or alternating from one side to the other, intermittent, and, most commonly, associated with lower back pain. Sometimes it feels like the testicle is pinched in the crotch of the underwear but trouser readjustment does not help. There may also be pain in the inguinal area but no nausea or other symptoms. Back pain may be concurrent or absent and some patients have a long history of low back pain. Onset of pain is commonly related to activity that would stress the low back such as lifting heavy objects. Other stresses that might cause low back pain are imaginative coital positions, jogging, sitting hunched over a computer, long car driving, or other such positions of unsupported seating posture that flattens the normal lumbar lordosis curve."

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.

Epididymitis makes up 1 in 144 visits for medical care (0.69 percent) in men 18 to 50 years old or 600,000 cases in males between 18 and 35 in the United States.

It occurs primarily in those 16 to 30 years of age and 51 to 70 years. As of 2008 there appears to be an increase in incidences in the United States that parallels an increase in reported cases of chlamydia and gonorrhea.

In medicine, ovarian vein syndrome is a rare (possibly not uncommon, certainly under-diagnosed) condition in which a dilated ovarian vein compresses the ureter (the tube that brings the urine from the kidney to the bladder). This causes chronic or colicky abdominal pain, back pain and/or pelvic pain. The pain can worsen on lying down or between ovulation and menstruation. There can also be an increased tendency towards urinary tract infection or pyelonephritis (kidney infection). The right ovarian vein is most commonly involved, although the disease can be left-sided or affect both sides. It is currently classified as a form of pelvic congestion syndrome.

A sperm granuloma is a lump of extravasated sperm that appears along the vasa deferentia or epididymides in vasectomized men. Sperm granulomas are rounded or irregular in shape, one millimeter to one centimeter or more, with a central mass of degenerating sperm surrounded by tissue containing blood vessels and immune system cells. Sperm granulomas can be either asymptomatic or symptomatic (i.e., either not painful or painful, respectively) (see post-vasectomy pain syndrome).

The vast majority of sperm granulomas in vasectomized men are present as a result of the pressure-induced changes of vasectomy.

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.

For some patients, the headaches may be related to general exertion. About 40% of patients with sexual headaches in one study also experienced headaches from non-sexual exertion. A pressor response to exercise has been suggested as a mechanism. For other patients, the pain appears to be specifically activated by sexual excitement and contraction of facial and neck muscles.

Sporadic case studies have linked sexual headaches to the use of certain drugs, including amiodarone, pseudoephedrine, birth control pills, and cannabis. It may be secondary to another condition, such as reversible cerebral vasoconstriction syndrome. It is associated with migraines.

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.

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".

Normally, the ovarian vein crosses over the ureter at the level of the fourth or fifth lumbar vertebral bone. The ureter itself courses over the external iliac artery and vein. Thus, these vessels can impinge on the ureter causing obstruction. The left ovarian vein ends in the renal vein whereas the right ovarian vein normally enters into the inferior vena cava. In the case of right ovarian vein syndrome, the vein often ends in the renal vein. This is thought to contribute to venous engorgement, in analogy to what is seen in varicoceles, which arise more commonly on the left side. The straight angle between the ovarian vein (or testicular vein in males in the case of varicocoele) and the renal vein has been proposed as a cause of decreased blood return.

A related diagnosis is "Nutcraker Syndrome" where the left renal vein is described as being compressed between the aorta and the superior mesenteric artery. This is reported to cause collateral flow paths to open up to drain the left kidney i.e. reversed flow (reflux caudally) in the left renal vein. Pelvic Congestion Syndrome, vaginal and vulval varices, lower limb varices are clinical sequelae. Virtually all such patient are female and have been pregnant, often multiply.

The ovarian vein often displays incompetent valves. This has been observed more often in women with a higher number of previous pregnancies. Pressure from the baby might hinder the return of blood through the ovarian vein. It has to be noted however that dilation of the urinary tract is a normal observation in pregnancy, due to mechanical compression and the hormonal action of progesterone. Ovarian vein dilatation might also follow venous thrombosis (clotting inside the vein).

Another proposed mechanism of obstruction is when the ovarian vein and ureter both run through a sheath of fibrous tissue, following a local inflammation. This could be seen as a localised form of retroperitoneal fibrosis.

Following obstruction, the ureter displays an abnormal peristalsis (contractions) towards the kidney instead of towards the bladder. This is thought to cause the colicky pain (similar to renal colic), and it is relieved after surgical decompression.

Vasitis nodosa is a complication experienced in approximately 66% of men who undergo vasectomy. It is a benign nodular thickening of the vas deferens, in which small offshoots proliferate, infiltrating surrounding tissue. It can be mistaken for low-grade adenocarcinoma by pathologists, and is implicated in late vasectomy failure.

One of the main causes is suggested to be excessive and repetitive straining during defecation. Other causes include weakness of the pelvic floor muscles (secondary to age related neuropathic degeneration or traumatic injury during pregnancy and labor.

The cause of POIS is unknown. Some doctors hypothesize that POIS is caused by an auto-immune reaction. Other doctors suspect a hormone imbalance as the cause. While other causes have been proposed as well, none of the proposed causes seem to fully explain the disease.

Despite its wasting and at times long-lasting effects, most cases resolve themselves and recovery is usually good in 18–24 months, depending on how old the person in question is. For instance, a six-year-old could have brachial neuritis for only around 6 months, but a person in their early fifties could have it for over 3 years.

The duct widening is commonly believed to be a result of secretory stasis, including stagnant colostrum, which also causes periductal inflammation and fibrosis. However, because nonspecific duct widening is common it might be also coincidental finding in many processes.

Smokers seem more often affected by duct ectasia "syndrome" although the reported results are not entirely consistent. The correlation with smoking status appears weaker than for subareolar abscess. Correlation with the actual duct widening is not known.

Both duct widening and duct ectasia syndrome are frequently bilateral, hence systemic causes are likely involved.

The term has several meanings on histological and symptomatic levels and on both levels "usage" overlaps with mastalgia, fibrocystic disease and specific sub- or superclasses of nonpuerperal mastitis. While this is not ideal for a definition it results from actual usage in international literature. Because research literature regarding duct ectasia is anything but abundant it is probably easiest to determine the exact meaning(s) intended by the respective authors on a case by case basis and this section can offer only a few hints.

Typical usage in North America is a synonym of nonpuerperal mastitis, including the special cases of granulomatous mastitis, comedo mastitis, subareolar abscess with or without squamous metaplasia of lactiferous ducts and fistulation.

Simple duct widening should be carefully distinguished from more complex histological changes.

Of the millions experiencing strokes worldwide, over 30,000 in the United States alone have developed some form of Dejerine–Roussy syndrome. 8% of all stroke patients will experience central pain syndrome, with 5% experiencing moderate to severe pain. The risk of developing Dejerine–Roussy syndrome is higher in older stroke patients, about 11% of stroke patients over the age of 80.

Studies have shown that the male partner cohabitating with a pregnant female will experience hormonal shifts in his prolactin, cortisol, estradiol, and testosterone levels, typically starting at the end of the first trimester and continuing through several weeks post-partum.

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.