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.

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.

Despite the similarity of name, an epispadias is not a type of hypospadias, and involves a problem with a different set of embryologic processes.

Women can also have this type of congenital malformation. Epispadias of the female may occur when the urethra develops too far anteriorly, exiting in the clitoris or even more forward. For females, this may not cause difficulty in urination but may cause problems with sexual satisfaction. Frequently, the clitoris is bifurcated at the site of urethral exit, and therefore clitoral sensation is less intense during sexual intercourse due to frequent stimulation during urination. However, with proper stimulation, using either manual or positional techniques, clitoral orgasm is definitely possible.

Most cases involve a small and bifid penis, which requires surgical closure soon after birth, often including a reconstruction of the urethra. Where it is part of a larger exstrophy, not only the urethra but also the bladder (bladder exstrophy) or the entire perineum (cloacal exstrophy) are open and exposed on birth, requiring closure.

Monorchism (also monorchidism) is the state of having only one testicle within the scrotum.

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.

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.

Many other less common conditions can lead to testicular pain. These include inguinal hernias, injury, hydroceles, and varicoceles among others. Testicular cancer is usually painless. Another potential cause is epididymal hypertension (also known as "blue balls").

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.

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.

Aphallia is a congenital malformation in which the phallus (penis or clitoris) is absent. It is the female counterpart of penile agenesis and testicular agenesis. The word is derived from the Greek "a-" for "not", and "phallos" for "penis". It is classified as an intersex condition.

A chordee may be caused by an underlying condition, such as a disorder of sex development or an intersex condition, or from a complication of circumcision, though some medical professionals do not consider it to be true chordee because the corporal bodies are normally formed. However, not all congenital chordee includes abnormal corpora, and case reports of damage to the corpus cavernosum from circumcision are noted in the literature; particularly as a complication of local anesthetic.

Chordee () is a condition in which the head of the penis curves downward or upward, at the junction of the head and shaft of the penis. The curvature is usually most obvious during erection, but resistance to straightening is often apparent in the flaccid state as well. In many cases but not all, chordee is associated with hypospadias. This is not the same condition as Peyronie's disease, which involves curvature of the shaft of the penis most commonly due to injury during adult life.

A bifid penis (or double penis) is a rare congenital defect where two genital tubercles develop.

Historically, males born with a bifid penis often underwent sex reassignment surgery, due to the difficulty of penile reconstruction. They were raised as girls, and often had reconstructive surgery to make them phenotypically female, coupled with female hormone replacement therapy. However, in recent years, this practice has fallen under heavy scrutiny due to both a high frequency of sexual dysfunction in gender converted children, and more advanced penile reconstruction techniques.

Many male marsupials naturally have a bifid penis, with left and right prongs that they insert into multiple vaginal canals simultaneously.

Aphallia has no known cause. It is not linked to deficient hormone amounts or action, but rather to a failure of the fetal genital tubercle to form between 3 and 6 weeks after conception. The urethra of an affected child opens on the perineum.

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.

Webbed penis, also called penis palmatus or penoscrotal fusion, is an acquired or congenital condition in which the scrotal skin extends onto the ventral penile shaft. The penile shaft is buried in scrotum or tethered to the scrotal midline by a fold or web of skin. The urethra and erectile bodies are usually normal. Webbed penis is usually asymptomatic, but the cosmetic appearance is often unacceptable. This condition may be corrected by surgical techniques.

In the congenital form, the deformity represents an abnormality of the attachment between the penis and the scrotum; the penis, the urethra, and the remainder of the scrotum typically are normal.

Webbed penis may also be acquired (iatrogenic) after circumcision or other penile surgery, resulting from excessive removal of ventral penile skin; the penis can retract into the scrotum, resulting in secondary phimosis (trapped penis).

One procedure for webbed penis is the insertion of a subcutaneous soft silicone implant under the penile skin. The procedure was developed by urologist James J. Elist.

Penile torsion is a fairly common congenital condition with male infants. It occurs up to about 1 in 80 newborn males. With this condition, the penis appears rotated on its axis, almost always to the left (counterclockwise).

Of the abnormal conditions associated with micropenis, most are conditions of reduced prenatal androgen production or effect, such as abnormal testicular development (testicular dysgenesis), Klinefelter syndrome, Leydig cell hypoplasia), specific defects of testosterone or dihydrotestosterone synthesis (17,20-lyase deficiency, 5α-reductase deficiency), androgen insensitivity syndromes, inadequate pituitary stimulation (gonadotropin deficiency), and other forms of congenital hypogonadism. Micropenis can also occur as part of many genetic malformation syndromes that do not involve the sex chromosomes. It is sometimes a sign of congenital growth-hormone deficiency or congenital hypopituitarism. Several homeobox genes affect penis and digit size without detectable hormone abnormalities.

In addition, in utero exposure to some estrogen based fertility drugs like diethylstilbestrol (DES) has been linked to genital abnormalities and/or a smaller than normal penis.

After evaluation to detect any of the conditions described above, micropenis can often be treated in infancy with injections of various hormones, such as human chorionic gonadotropin and testosterone.

Most eight- to fourteen-year-old boys referred for micropenis do not have the micropenis condition. Such concerns are usually explained by one of the following:

- a penis concealed in suprapubic fat (extra fat around the mons pubis)

- a large body and frame for which a prepubertal penis simply appears too small

- delayed puberty with every reason to expect good future growth

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.

Micropenis is an unusually small penis. A common criterion is a dorsal (measured on top) erect penile length of at least 2.5 standard deviations smaller than the mean human penis size, or smaller than about for an adult when compared with an average erection of . The condition is usually recognized shortly after birth. The term is most often used medically when the rest of the penis, scrotum, and perineum are without ambiguity, such as hypospadias. Micropenis occurs in about 0.6% of males.

The classic manifestation of bladder exstrophy presents with:

- A defect in the abdominal wall occupied by both the exstrophied bladder as well as a portion of the urethra

- A flattened puborectal sling

- Separation of the pubic symphysis

- Shortening of a pubic rami

- External rotation of the pelvis.

Females frequently have a displaced and narrowed vaginal orifice, a clitoris, and divergent labia.

Patients with ovarian torsion often present with sudden onset of sharp and usually unilateral lower abdominal pain, in 70% of cases accompanied by nausea and vomiting.

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.