Hypospadias is usually diagnosed in the newborn nursery by the characteristic appearance of the penis. The urinary opening (“meatus”) is lower than normal, and most children have only partial development of the foreskin, lacking the normal covering for the glans on the underside. The abnormal “hooded” foreskin calls attention to the condition. However, not all newborns with partial foreskin development have hypospadias, as some have a normal urinary opening with a hooded foreskin, which is called “chordee without hypospadias”.

Megameatus with intact prepuce variant of hypospadias occurs when the foreskin is normal and the hypospadias is concealed. The condition is discovered during newborn circumcision or later in childhood when the foreskin begins to retract. A newborn with normal-appearing foreskin and a straight penis who is discovered to have hypospadias after a circumcision was started can have circumcision completed without worry for jeopardizing future hypospadias repair. Hypospadias is almost never discovered after a circumcision.

Hypospadias is a congenital disorder of the urethra where the urinary opening is not at the usual location on the head of the penis. It is the second-most common birth abnormality of the male reproductive system, affecting about one of every 250 males at birth. In roughly 90% of cases, the opening (meatus) is on or near the head of the penis (glans), referred to as distal hypospadias, while the remainder have proximal hypospadias with a meatus near or within the scrotum. Shiny tissue seen extending from the meatus to the tip of the glans, which would have made the urinary channel, is referred to as the urethral plate.

In most cases, the foreskin is also underdeveloped and does not wrap completely around the penis, leaving the underside of the glans penis uncovered. Also, a downward bending of the penis, commonly referred to as chordee, may occur. This is found in 10% of distal hypospadias and 50% of proximal hypospadias at the time of surgery. The scrotum may be higher than usual to either side of the penis, called penoscrotal transposition, adding to the abnormal overall appearance.

Hypospadias is thought to result from failure of the urinary channel to completely tubularize to the end of the penis; the cause is not known. Most often, it is the only abnormal finding, although in about 10% of cases, hypospadias may be part of a syndrome with multiple abnormalities.

The most common associated defect is an undescended testicle, which has been reported in around 3% of infants with distal hypospadias and 10% of those having proximal hypospadias. The combination of hypospadias and an undescended testicle sometimes indicates a disorder of sexual differentiation, and so additional testing may be recommended. Otherwise no blood tests or X-rays are routinely needed in newborns with hypospadias.

Hypospadias can be a symptom or indication of an intersex condition but the presence of hypospadias alone is not enough to classify as intersex. In most cases, hypospadias is not associated with any condition.

PPSH usually consists of:

- a phallus midway in size between penis and clitoris,

- a chordee tethering it to the perineum,

- a urethral opening usually on the perineum (the hypospadias),

- and an incompletely closed urogenital opening, which resembles a small and shallow vagina.

Testes are often palpable in the scrotum or inguinal canals, and the karyotype is XY. In most cases there are no internal female structures such as a uterus or other Müllerian duct derivatives.

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.

It is usually considered a congenital malformation of unknown cause. Since at an early stage of fetal development the penis is curved downward, it has been proposed that chordee results from an arrest of penile development at that stage.

The curvature of a chordee can involve

1. tethering of the skin with urethra and corpora of normal size;

2. curvature induced by fibrosis and contracture of the fascial tissue (Buck's fascia or dartos) surrounding the urethra;

3. disproportionately large corpora in relation to the urethral length without other demonstrable abnormality of either; or

4. a short, fibrotic urethra that tethers the penis downward (the least common type).

Severe degrees of chordee are usually associated with hypospadias, but mild degrees of curvature may occur in many otherwise normal males. When the curved penis is small and accompanied by hypospadias, deficiency of prenatal androgen effect can be inferred.

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.

Pseudovaginal perineoscrotal hypospadias (PPSH) refers to a configuration of the external genitalia of an infant. In a sense, this configuration is roughly midway between normal male genitalia and normal female genitalia in structure and appearance. It is a relatively common form of genital ambiguity caused by undervirilization of genetic males due to several different intersex conditions.

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.

An older system of classification structures polyorchidism into similar types, but with no subdivision between connected and disconnected testicles:

- Type 1: The testicle lacks an epididymis and vas deferens and has no connection to the other testicles.

- Type 2: The supernumerary testicle shares the epididymis and the vas deferens of the other testicles.

- Type 3: The supernumerary testicle has its own epididymis and shares a vas deferens.

- Type 4: Complete duplication of the testicle, epididymis and vas deferens.

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.

Cryptorchidism is the absence of one or both testes from the scrotum. It is the most common birth defect of the male genital. About 3% of full-term and 30% of premature infant boys are born with at least one undescended testis. However, about 80% of cryptorchid testes descend by the first year of life (the majority within three months), making the true incidence of cryptorchidism around 1% overall. Cryptorchidism may develop after infancy, sometimes as late as young adulthood, but that is exceptional.

Cryptorchidism is distinct from monorchism, the condition of having only one testicle. The condition may occur on one or both sides; it more commonly affects the right testis.

A testis absent from the normal scrotal position may be:

1. anywhere along the "path of descent" from high in the posterior (retroperitoneal) abdomen, just below the kidney, to the inguinal ring;

2. in the inguinal canal;

3. "ectopic", having "wandered" from the path of descent, usually outside the inguinal canal and sometimes even under the skin of the thigh, the perineum, the opposite scrotum, or the femoral canal;

4. undeveloped ("hypoplastic") or severely abnormal ("dysgenetic");

5. missing (also see anorchia).

About two-thirds of cases without other abnormalities are unilateral; most of the other third involve both testes. In 90% of cases an undescended testis can be felt in the inguinal canal. In a small minority of cases missing testes may be found in the abdomen or appear to be nonexistent (truly "hidden").

Undescended testes are associated with reduced fertility, increased risk of testicular germ cell tumors and psychological problems when the boy is grown. Undescended testes are also more susceptible to testicular torsion (and subsequent infarction) and inguinal hernias. Without intervention, an undescended testicle will usually descend during the first year of life, but to reduce these risks, undescended testes can be brought into the scrotum in infancy by a surgical procedure called an orchiopexy.

Although cryptorchidism nearly always refers to "congenital" absence or maldescent, a testis observed in the scrotum in early infancy can occasionally "reascend" (move back up) into the inguinal canal. A testis which can readily move or be moved between the scrotum and canal is referred to as "retractile". The word is from the Greek "κρυπτός", "kryptos", meaning hidden "ὄρχις", "orchis", meaning testicle.

Cryptorchidism, hypospadias, testicular cancer and poor semen quality make up the syndrome known as testicular dysgenesis syndrome.

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.

Many men who were born with undescended testes have reduced fertility, even after orchiopexy in infancy. The reduction with unilateral cryptorchidism is subtle, with a reported infertility rate of about 10%, compared with about 6% reported by the same study for the general population of adult men.

The fertility reduction after orchiopexy for bilateral cryptorchidism is more marked, about 38%, or 6 times that of the general population. The basis for the universal recommendation for early surgery is research showing degeneration of spermatogenic tissue and reduced spermatogonia counts after the second year of life in undescended testes. The degree to which this is prevented or improved by early orchiopexy is still uncertain.

Scrotal ultrasonography and transrectal ultrasonography (TRUS) are useful in detecting uni- or bilateral CBAVD, which may be associated with visible abnormalities or agenesis of the epididymis, seminal vesicles or kidneys.

If a colostomy is not performed immediately after birth, patients with rectovestibular fistulae may present later in life with complications including severe constipation and megacolon (abnormal dilation of the colon), requiring colostomy or further surgery.

Mild cases may simply produce a sense of pressure or protrusion within the vagina, and the occasional feeling that the rectum has not been completely emptied after a bowel movement. Moderate cases may involve difficulty passing stool (because the attempt to evacuate pushes the stool into the rectocele instead of out through the anus), discomfort or pain during evacuation or intercourse, constipation, and a general sensation that something is "falling down" or "falling out" within the pelvis. Severe cases may cause vaginal bleeding, intermittent fecal incontinence, or even the prolapse of the bulge through the mouth of the vagina, or rectal prolapse through the anus. Digital evacuation, or, manual pushing, on the posterior wall of the vagina helps to aid in bowel movement in a majority of cases of rectocele. Rectocele can be a cause of symptoms of obstructed defecation.

The vas deferens connect the sperm-producing testicles to the penis. Therefore, those who are missing both vas deferens are typically able to create sperm but are unable to transport them appropriately. Their semen does not contain sperm, a condition known as azoospermia.

Perineal hernia is a hernia involving the perineum (pelvic floor). The hernia may contain fluid, fat, any part of the intestine, the rectum, or the bladder. It is known to occur in humans, dogs, and other mammals, and often appears as a sudden swelling to one side (sometimes both sides) of the anus.

A common cause of perineal hernia is surgery involving the perineum. Perineal hernia can be caused also by excessive straining to defecate (tenesmus). Other causes include prostate or urinary disease, constipation, anal sac disease (in dogs), and diarrhea. Atrophy of the levator ani muscle and disease of the pudendal nerve may also contribute to a perineal hernia.

A rectocele ( ) or posterior vaginal wall prolapse results when the rectum herniates into or forms a bulge in the vagina. Two common causes of this defect is: childbirth, and hysterectomy. Rectocele also tends occur with other forms of pelvic organ prolapse such as enterocele, sigmoidocele and cystocele.

Although the term applies most often to this condition in females, males can also develop. Rectoceles in men are uncommon, and associated with prostatectomy.

In humans, a major cause of perineal hernia is perineal surgery without adequate reconstruction. In some cases, particularly surgeries to remove the coccyx and distal sacrum, adequate reconstruction is very difficult to achieve. The posterior perineum is a preferred point of access for surgery in the pelvic cavity, particularly in the presacral space. Surgeries here include repair of rectal prolapse and anterior meningocele, radical perineal prostatectomy, removal of tumors including sacrococcygeal teratoma, and coccygectomy. Perineal hernia is a common complication of coccygectomy in adults, but not in infants and children (see coccygectomy).

The standard surgical technique for repair of perineal hernia uses a prosthetic mesh, but this technique has a high rate of failure due to insufficient anchoring. Promising new techniques to reduce the rate of failure include an orthopedic anchoring system, a gluteus maximus muscle flap, an acellular human dermis graft, and an acellular pig collagen graft.

A rectovestibular fistula, also referred to simply as a vestibular fistula, is an anorectal congenital disorder where an abnormal connection (fistula) exists between the rectum and the vulval vestibule of the female genitalia.

If the fistula occurs within the hymen, it is known as a rectovaginal fistula, a much rarer condition.

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

Bulbar urethral necrosis is a problem that can occur after a pelvic fracture associated urethral distraction defect (PFUDD).