Untreated, acute epididymitis's major complications are abscess formation and testicular infarction. Chronic epididymitis can lead to permanent damage or even destruction of the epididymis and testicle (resulting in infertility and/or hypogonadism), and infection may spread to any other organ or system of the body. Chronic pain is also an associated complication for untreated chronic epididymitis.

Those ages 15 to 35 are most commonly affected. The acute form usually develops over the course of several days, with pain and swelling frequently in only one testis, which will hang low in the scrotum. There will often be a recent history of dysuria or urethral discharge. Fever is also a common symptom. In the chronic version, the patient may have painful point tenderness but may or may not have an irregular epididymis upon palpation, though palpation may reveal an indurated epididymis. A scrotal ultrasound may reveal problems with the epididymis, but such an ultrasound may also show nothing unusual. The majority of patients who present with chronic epididymitis have had symptoms for over five years.

Testicular torsion usually presents with an acute onset of diffuse testicular pain and tenderness of less than 6 hrs of duration. There is often an absent or decreased cremasteric reflex, the testicle is elevated, and often is horizontal. It occurs annually in about 1 in 4000 males before 25 years of age, is most frequent among adolescents ( 65% of cases presenting between 12 – 18 years of age ), and is rare after 35 years of age. Because it can lead to necrosis within a few hours, it is considered a surgical emergency. Another version of this condition is a chronic illness called intermittent testicular torsion (ITT) which is characterized by recurrent rapid acute onset of pain in one testis which will temporarily assume a horizontal or elevated position in the scrotum similar to that of a full torsion followed by eventual spontaneous detortion and rapid solution of pain. Nausea or vomiting may also occur.

Epididymitis occurs when there is inflammation of the epididymis (a curved structure at the back of the testicle). This condition usually presents with gradual onset of varying degrees of pain, and the scrotum may be red, warm and swollen. It is often accompanied by symptoms of a urinary tract infection, fever, and in over half of cases it presents in combination with orchitis. In those between the ages of 14 to 35 it is usually caused by either gonorrhea or chlamydia. In people either older or younger E. coli is the most common bacterial infection. Treatment involves the use of antibiotics.

Symptoms of orchitis are similar to those of testicular torsion. These can include:

- hematospermia (blood in the semen)

- hematuria (blood in the urine)

- severe pain

- visible swelling of a testicle or testicles and often the inguinal lymph nodes on the affected side.

The symptoms of urethritis can include pain or a burning sensation upon urination (dysuria), a white/cloudy discharge and a feeling that one needs to pass urine frequently. For men, the signs and symptoms are discharge from the penis, burning or pain when urinating, itching, irritation, or tenderness. In women, the signs and symptoms are discharge from vagina, burning or pain when urinating, anal or oral infections, abdominal pain, or abnormal vaginal bleeding, which may be an indication that the infection has progressed to Pelvic Inflammatory Disease.

NGU is transmitted by touching the mouth, penis, vagina or anus by penis, vagina or anus of a person who has NGU.

NGU is more common in men than women. Men may have a discharge (strange liquid) from the penis, pain when urinating, and itching, irritation or tenderness around the opening of the penis. Women might not have any symptoms and may not know they have NGU until severe problems occur. Women might have discharge from the vagina, burning or pain when urinating, pain in the abdominal (stomach) area, or bleeding from the vagina that is not from a monthly period. (This may be an sign that NGU has become worse and turned into Pelvic Inflammatory Disease, or PID).

Orchitis can be related to epididymitis infection that has spread to the testicles (then called "epididymo-orchitis"), sometimes caused by the sexually transmitted diseases chlamydia and gonorrhea. It has also been reported in cases of males infected with brucellosis. Orchitis can also be seen during active mumps, particularly in adolescent boys.

Ischemic orchitis may result from damage to the blood vessels of the spermatic cord during inguinal herniorrhaphy, and may in the worst event lead to testicular atrophy.

Potential complications include:

- obstruction of the epididymis

- impairment of spermatogenesis

- impairmentment of sperm function

- induction of sperm auto-antibodies

- dysfunctions of the male accessory glands

These complications can result in

sexual dysfunction and male subfertility.

The main infectious agents are Enterobacteriaceae (such as Escherichia coli and Klebsiella), Neisseria gonorrhoeae and Chlamydia trachomatis.

One study has shown that men with MAGI who have lower serum levels of total testosterone tend to have a more complicated form of MAGI, such as involving more than one site, than those with normal levels.

Urethritis can be caused by mechanical injury (from a urinary catheter or a cystoscope), or by an irritating chemical (antiseptics or some spermicides).

Post-vasectomy pain syndrome is a chronic and sometimes debilitating genital pain condition that may develop immediately or several years after vasectomy. Because this condition is a syndrome, there is no single treatment method, therefore efforts focus on mitigating/relieving the individual patient's specific pain. When pain in the epididymides is the primary symptom, post-vasectomy pain syndrome is often described as congestive epididymitis.

Any of the aforementioned pain conditions/syndromes can persist for years after vasectomy and affect as many as one in three vasectomized men. The range of PVPS pain can be mild/annoying to the less-likely extreme debilitating pain experienced by a smaller number of sufferers in this group. There is a continuum of pain severity between these two extremes. Pain is thought to be caused by any of the following, either singularly or in combination: testicular backpressure, overfull epididymides, chronic inflammation, fibrosis, sperm granulomas, and nerve entrapment. Pain can be present continuously in the form of orchialgia and/or congestive epididymitis or it can be situational, such as pain during intercourse, ejaculation or physical exertion.

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.

Testicular torsion usually presents with sudden, severe, testicular pain (in groin and lower abdomen) and tenderness. There is often associated nausea and vomiting. The testis may be higher than its normal position. Mild pyrexia and redness of overlying area may be found.

Some of the symptoms are similar to epididymitis though epididymitis may be characterized by discoloration and swelling of the testis, often with fever, while the cremasteric reflex is usually present. Testicular torsion, or more probably impending testicular infarction, can also produce a low-grade fever.

There is often an absent or decreased cremasteric reflex.

Spermatoceles can be discovered as incidental scrotal masses found on physical examination by a physician. They may also be discovered by self-inspection of the scrotum and testicles.

Finding a painless, cystic mass at the head of the epididymis, that transilluminates and can be clearly differentiated from the testicle, is generally sufficient. If uncertainty exists, ultrasonography of the scrotum can confirm if it is spermatocele.

If an individual finds what he suspects to be a spermatocele, he is advised to consult a urologist.

Polyorchidism occurs in two primary forms: Type A and Type B.

- Type A: The supernumerary testicle is connected to a vas deferens. These testicles are usually reproductively functional. Type A is further subdivided into:

- Type A1: Complete duplication of the testicle, epididymis and vas deferens.

- Type A2: The supernumerary testicle has its own epididymis and shares a vas deferens.

- Type A3: The supernumerary testicle shares the epididymis and the vas deferens of the other testicles.

- Type B: The supernumerary testicle is not connected to a vas deferens and is therefore not reproductively functional. Type B is further subdivided into:

- Type B1: The supernumerary testicle has its own epididymis but is not connected to a vas deferens

- Type B2: The supernumerary testicle consists only of testicular tissue.

Type A3 is the most common form of polyorchidism, and types A2 and A3 together account for more than 90% of cases. In 65% of cases, the supernumerary testicle is found in the left scrotal sac.

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.

This type of torsion is the most common cause of acute scrotal pain in boys ages 7–14. Its appearance is similar to that of testicular torsion but the onset of pain is more gradual. Palpation reveals a small firm nodule on the upper portion of the testis which displays a characteristic "blue dot sign". This is the appendix of the testis which has become discolored and is noticeably blue through the skin. Unlike other torsions, however, the cremasteric reflex is still active. Typical treatment involves the use of over-the-counter analgesics and the condition resolves within 2–3 days.

Odynorgasmia, or painful ejaculation, is a physical syndrome described by pain or burning sensation of the urethra or perineum during or following ejaculation. Causes include infections associated with urethritis, prostatitis, epididymitis, as well as use of anti-depressants.

In men, those with a chlamydial infection show symptoms of infectious inflammation of the urethra in about 50% of cases. Symptoms that may occur include: a painful or burning sensation when urinating, an unusual discharge from the penis, testicular pain or swelling, or fever. If left untreated, chlamydia in men can spread to the testicles causing epididymitis, which in rare cases can lead to sterility if not treated. Chlamydia is also a potential cause of prostatic inflammation in men, although the exact relevance in prostatitis is difficult to ascertain due to possible contamination from urethritis.

Bacteria and yeast, including those naturally occurring as part of the human microbiome, can travel along urinary catheters and cause an infection in the bladder, kidneys, and other organs connected to the urinary tract.

CAUTI can lead to complications such as prostatitis, epididymitis, and orchitis in men, and cystitis, pyelonephritis, gram-negative bacteremia, endocarditis, vertebral osteomyelitis, septic arthritis, endophthalmitis, and meningitis in all patients. Complications associated with CAUTI cause discomfort to the patient, prolonged hospital stay, and increased cost and mortality. It has been estimated that more than 13,000 deaths are associated with UTIs annually. Estimated > 560,000 nosocomial UTIs annually.

Catheter-associated urinary tract Infection, or CAUTI, is a urinary tract infection associated with urinary catheter use.

Chlamydia may also cause reactive arthritis—the triad of arthritis, conjunctivitis and urethral inflammation—especially in young men. About 15,000 men develop reactive arthritis due to chlamydia infection each year in the U.S., and about 5,000 are permanently affected by it. It can occur in both sexes, though is more common in men.

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.