Degloving and avulsion injuries involve the removal of the penis skin, which is a serious medical emergency. Treatment of these injuries involves either closure of the torn skin, or a skin graft to replace the skin lost in the injury. Skin grafts are constructed to attempt to preserve erectile function and sensation.

Penile fractures are the result of rupture of the tunica albuginea. They are fairly rare and can co-occur with partial or complete urethral rupture, though this is rare. Urethral damage occurs in 10–38% of cases. Fractures are treated with emergency surgery, and can be diagnosed with ultrasound, especially in pediatric cases. Penile fractures are caused by trauma to the erect penis, typically by suddenly bending it laterally during penetrative intercourse with the receptive partner on top of the penetrating partner, or during masturbation. They can be diagnosed by the "eggplant sign" and are characterized by a loud popping sound at the time of the injury, the result of the tunica albuginea rupturing. Other symptoms include severe pain, loss of erection, and swelling. Symptoms of urethral injury include hematuria, blood at the meatus, and dysuria. If left untreated, complications result in 28–53% of cases; these include permanent curvature of the penis, fistula, urethral diverticulum, priapism, and erectile dysfunction.

Vulvar trauma is more common in prepubertal children due to small labial fat pads and more physical activity. Adults are more protected. Though some injuries are serious, most are accidental minor blunt traumas. The most common type of injury is a straddle injury, which can be incurred through normal activities like bicycle riding. Due to the vascularity of the vulva, it may form a large hematoma when injured. The vulva can also be injured through sexual assault. Vulvar trauma can occur concurrently with vaginal trauma, especially if a sharp object is involved.

A popping or cracking sound, significant pain, swelling, immediate loss of erection leading to flaccidity, and skin hematoma of various sizes are commonly associated with the sexual event.

Vaginal trauma can occur when something is inserted into the vagina, for example, a sharp object, causing penetrating trauma.

Penile fracture is rupture of one or both of the "tunica albuginea", the fibrous coverings that envelop the penis's "corpora cavernosa". It is caused by rapid blunt force to an erect penis, usually during vaginal intercourse, or aggressive masturbation. It sometimes also involves partial or complete rupture of the urethra or injury to the dorsal nerves, veins and arteries.

Paraphimosis is usually caused by medical professionals or parents who handle the foreskin improperly: The foreskin may be retracted during penile examination, penile cleaning, urethral catheterization, or cystoscopy; if the foreskin is left retracted for a long period, some of the foreskin tissue may become edematous (swollen with fluid), which makes subsequent reduction of the foreskin difficult.

Paraphimosis is an uncommon medical condition in which the foreskin of a penis becomes trapped behind the glans penis, and cannot be "reduced" (pulled back to its normal flaccid position covering the glans). If this condition persists for several hours or there is any sign of a lack of blood flow, paraphimosis should be treated as a medical emergency, as it can result in gangrene.

Rupture of the urethra is an uncommon result of penile injury, incorrect catheter insertion, straddle injury, or pelvic girdle fracture. The urethra, the muscular tube that allows for urination, may be damaged by trauma. When urethral rupture occurs, urine may extravasate (escape) into the surrounding tissues. The membranous urethra is most likely to be injured in pelvic fractures, allowing urine and blood to enter the deep perineal space and subperitoneal spaces via the genital hiatus. The spongy urethra is most likely to be injured with a catheter or in a straddle injury, allowing urine and blood to escape into the scrotum, the penis, and the superficial peritoneal space. Urethral rupture may be diagnosed with a cystourethrogram. Due to the tight adherence of the fascia lata, urine from a urethral rupture cannot spread into the thighs.

Buried penis (also known as hidden penis) is a congenital or acquired condition, in which the penis is partially or completely hidden below the surface of the skin. It can lead to obstruction of urinary stream, poor hygiene, soft tissue infection, phimosis, and inhibition of normal sexual function. Congenital causes include maldevelopment of penile shaft skin, whereas acquired conditions include morbid obesity, overlaying abdominal fat, or penile injury. Adults with a buried penis will either live with their condition or undergo weight-loss programs. However, weight-loss programs are slow and often do not "unbury" the penis; furthermore, poor hygiene from pooling of urine can lead to soft tissue infection. Patients will eventually need definitive reconstructive surgery and more urgent surgery if infection is present. Surgeons who manage this condition are either reconstructive urologic surgeons or plastic surgeons.

Sclerosing lymphangitis is a skin condition characterized by a cordlike structure encircling the coronal sulcus of the penis, or running the length of the shaft, that has been attributed to trauma during vigorous sexual play.

Nonvenereal sclerosing lymphangitis is a rare penile lesion consisting of a minimally tender, indurated cord involving the coronal sulcus and occasionally adjacent distal penile skin. This disorder most often occurs after vigorous sexual activity and resolves spontaneously.

Etiology of Sclerosing lymphangitis is unknown but has been postulated to be secondary to thrombosis of lymphatic vessels. Spontaneous recovery can occur anywhere within a couple weeks to several months.

Although it is commonly recommended the patient abstain from any sexual activitiy during the recovery, there is no evidence that this expedites recovery nor that not abstaining worsens the condition.

Frenulum breve, or short frenulum, is a condition in which the frenulum of the penis, which is an elastic band of tissue under the glans penis that connects to the foreskin and helps contract it over the glans, is too short and thus restricts the movement of the foreskin. The frenulum should normally be sufficiently long and supple to allow for the full retraction of the foreskin so that it lies smoothly back on the shaft of the erect penis.

The penile frenulum is comparable to the tongue's frenulum between the tongue's lower surface and the lower jaw, or the frenulum between the upper lip and the outside of the upper gum.

Frenulum breve may be complicated by tearing of the frenulum during sexual or other activity and is a cause of dyspareunia. It may lead to erroneous labelling of the sufferer as having psychosexual problems. The torn frenulum may result in healing with scar tissue that is less flexible after the incident causing further difficulties. However, this tearing can also solve the problem, healing such that the frenulum is longer and therefore no longer problematic. The diagnosis of frenulum breve is almost always confused with that of phimosis and a generally tight foreskin, since the symptom is difficulty retracting the foreskin. Most men with phimosis also have frenulum breve to a certain extent.

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

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.

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

Symptoms can include:

- First signs – small red erosions on the glans

- Redness of the foreskin

- Redness of the penis

- Other rashes on the head of the penis

- Foul smelling discharge

- Painful foreskin and penis

A pelvic fracture can cause the urethra to separate, leading to a variable length of scar that can severely hamper the ability to urinate normally. The urethra is a tubular conduit that transports urine out of the bladder. The bulbar urethra is a segment of the male urethra that is in between the penile urethra and the membrano-prostatic urethra that typically has a robust blood supply. This blood supply includes antegrade flow from the paired bulbar arteries and circumflex arteries, and retrograde flow from the paired dorsal arteries of the penis.

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.

The hallmark sign of urethral stricture is a weak urinary stream. Other symptoms include:

- Splaying of the urinary stream

- Urinary frequency

- Urinary urgency

- Straining to urinate

- Pain during urination

- Urinary tract infection

- Prostatitis

- Inability to completely empty the bladder.

Some patients with severe urethral strictures are completely unable to urinate. This is referred to as acute urinary retention, and is a medical emergency. Hydronephrosis and renal failure may also occur.

Recurrent bouts of balanitis may cause scarring of the preputial orifice; the reduced elasticity may lead to pathologic phimosis.

A urethral stricture is a narrowing of the urethra caused by injury, instrumentation, infection and certain non-infectious forms of urethritis.

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.

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 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.