Penetrating and blunt traumas combined make up approximately 90% of all civilian penile injuries (45% each), with burns and other accidents making up the remaining 10%.

The causes of penile injury are mostly the same as other causes of trauma; however, penile injury is more likely to occur during sexual intercourse and masturbation than other traumas. Nocturnal erections and sleeping positions can be another cause of penile injury. Industrial and automobile accidents can also cause penile injury. Self-injury may also affect the penis.

Penile fracture is a relatively uncommon clinical condition. Vaginal intercourse and aggressive masturbation are the most common causes. A 2014 study of accident and emergency records at three hospitals in Campinas, Brazil, showed that woman on top positions caused the greatest risk with the missionary position being the safest. The research conjectured that when a woman is on top, she usually controls the movement and her entire body weight lands on the erect penis. She is not able to interrupt movement when the penis suffers a misaligned penetration. Conversely, when the man is controlling the movement, he has better chances of stopping the penetration thrusts in response to pain, minimizing harm to himself.

The practice of "taqaandan" (also "taghaandan") also puts men at risk of penile fracture. Taqaandan, which comes from a Kurdish word meaning "to click", involves bending the top part of the erect penis while holding the lower part of the shaft in place, until a click is heard and felt. Taqaandan is said to be painless and has been compared to cracking one's knuckles, but the practice of taqaandan has led to an increase in the prevalence of penile fractures in western Iran. Taqaandan may be performed to achieve detumescence.

Penile trauma can take several forms. Abrasions can be caused by a zipper injury, and fractures can be caused by sexual activity.

Penile fracture is a medical emergency, and emergency surgical repair is the usual treatment. Delay in seeking treatment increases the complication rate. Non-surgical approaches result in 10–50% complication rates including erectile dysfunction, permanent penile curvature, damage to the urethra and pain during sexual intercourse, while operatively treated patients experience an 11% complication rate.

In some cases, retrograde urethrogram may be performed to rule out concurrent urethral injury.

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

Paraphimosis can be avoided by bringing the foreskin back into its normal, forward, non-retracted position after retraction is no longer necessary (for instance, after cleaning the glans penis or placing a Foley catheter). Phimosis (both pathologic and normal childhood physiologic forms) is a risk factor for paraphimosis; "physiologic" phimosis resolves naturally as a child matures, but it may be advisable to treat "pathologic" phimosis via long-term stretching or elective surgical techniques (such as preputioplasty to loosen the preputial orifice or circumcision to amputate the foreskin tissue partially or completely).

The foreskin responds to the application of tension to cause expansion by creating new skin cells though the process of mitosis. The tissue expansion is permanent. Non-surgical stretching of the foreskin may be used to widen a narrow, non-retractable foreskin. Stretching may be combined with the use of a steroid cream. Beaugé recommends manual stretching for young males in preference to circumcision as a treatment for non-retractile foreskin because of the preservation of sexual sensation.

Paraphimosis can often be effectively treated by manual manipulation of the swollen foreskin tissue. This involves compressing the glans and moving the foreskin back to its normal position, perhaps with the aid of a lubricant, cold compression, and local anesthesia as necessary. If this fails, the tight edematous band of tissue can be relieved surgically with a dorsal slit or circumcision. An alternative method, the Dundee technique, entails placing multiple punctures in the swollen foreskin with a fine needle, and then expressing the edema fluid by manual pressure. According to Ghory and Sharma, treatment by circumcision may be elected as "a last resort, to be performed by a urologist". Other experts recommend delaying elective circumcision until after paraphimosis has been resolved.

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.

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.

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.

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.

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.

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.

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.

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.

Occurring at a rate between 1 in 10,000 to 1 in 50,000 with a male-to-female ratio of 2.3-6:1, bladder exstrophy is relatively rare. For those individuals with bladder exstrophy who maintain their ability to reproduce, the risk of bladder exstrophy in their children is approximately 500-fold greater than the general population.

The treatment for PFUDDs is scar excision and primary anastomosis, which means reconnecting the two ends of the urethra that were severed during the pelvic injury. Most patients do well with this but occasionally, stricture of the repair recurs and the patients may require redo surgery.

Surgery involves making an incision between the anus and scrotum (perineal incision) and dissecting out the bulbar urethra and locating the scar and membranoprostatic urethra. Dissecting the bulbar urethra destroys the antegrade blood flow. However, this urethra still does well since in still gets retrograde blood flow from the dorsal arteries. When patients have erectile dysfunction, the dorsal arteries do not work well and therefore the bulbar urethra does not get a good blood supply.

Even with successful surgery, patients may have long-term problems with:

- incontinence, where serious usually treated with some form of continent urinary diversion such as the Mitrofanoff

- depression and psycho-social complications

- sexual dysfunction

Urethral strictures most commonly result from injury, urethral instrumentation, infection, non-infectious inflammatory conditions of the urethra, and after prior hypospadias surgery. Less common causes include congenital urethral strictures and those resulting from malignancy.

Urethral strictures after blunt trauma can generally be divided into two sub-types;

- Pelvic fracture-associated urethral disruption occurs in as many as 15% of severe pelvic fractures. These injuries are typically managed with suprapubic tube placement and delayed urethroplasty 3 months later. Early endoscopic realignment may be used in select cases instead of a suprapubic tube, but these patients should be monitored closely as vast majority of them will require urethroplasty.

- Blunt trauma to the perineum compresses the bulbar urethra against the pubic symphysis, causing a "crush" injury. These patients are typically treated with suprapubic tube and delayed urethroplasty.

Other specific causes of urethral stricture include:

- Instrumentation (e.g., after transurethral resection of prostate, transurethral resection of bladder tumor, or endoscopic kidney surgery)

- Infection (typically with Gonorrhea)

- Lichen sclerosus

- Surgery to address hypospadias can result in a delayed urethral stricture, even decades after the original surgery.

The numbers of women with SCI giving birth and having healthy babies are increasing. Around a half to two-thirds of women with SCI report they might want to have children, and 14–20% do get pregnant at least once. Although female fertility is not usually permanently reduced by SCI, there is a stress response that can happen immediately post-injury that alters levels of fertility-related hormones in the body. In about half of women, menstruation stops after the injury but then returns within an average of five months—it returns within a year for a large majority. After menstruation returns, women with SCI become pregnant at a rate close to that of the rest of the population.

Pregnancy is associated with greater-than-normal risks in women with SCI, among them increased risk of deep vein thrombosis, respiratory infection, and urinary tract infection. Considerations exist such as maintaining proper positioning in a wheelchair, prevention of pressure sores, and increased difficulty moving due to weight gain and changes in center of balance. Assistive devices may need to be altered and medications changed.

For women with injuries above T6, a risk during labor and delivery that threatens both mother and fetus is autonomic dysreflexia, in which the blood pressure increases to dangerous levels high enough to cause potentially deadly stroke. Drugs such as nifedipine and captopril can be used to manage an episode if it occurs, and epidural anesthesia helps although it is not very reliable in women with SCI. Anesthesia is used for labor and delivery even for women without sensation, who may only experience contractions as abdominal discomfort, increased spasticity, and episodes of autonomic dysreflexia. Reduced sensation in the pelvic area means women with SCI usually have less painful delivery; in fact, they may fail to realize when they go into labor. If there are deformities in the pelvis or spine caesarian section may be necessary. Babies of women with SCI are more likely to be born prematurely, and, premature or not, they are more likely to be small for their gestational time.

Inflammation has many possible causes, including irritation by environmental substances, physical trauma, and infection such as bacterial, viral, or fungal. Some of these infections are sexually transmitted diseases.

It is less common among people who are circumcised as in many cases the foreskin contributes to the disease. Both not enough cleaning and too much cleaning can cause problems. Diabetes can make balanitis more likely, especially if the blood sugar is poorly controlled.

It is important to exclude other causes of similar symptoms such as penile cancer.

The use of bioengineered urethral tissue is promising, but still in the early stages. The Wake Forest Institute of Regenerative Medicine has pioneered the first bioengineered human urethra, and in 2006 implanted urethral tissue grown on bioabsorbable scaffolding (approximating the size and shape of the affected areas) in five young (human) males who suffered from congenital defects, physical trauma, or an unspecified disorder necessitating urethral reconstruction. As of March, 2011, all five recipients report the transplants have functioned well.

Common causes of head injury are motor vehicle traffic collisions, home and occupational accidents, falls, and assaults. Wilson's disease has also been indicative of head injury. According to the United States CDC, 32% of traumatic brain injuries (another, more specific, term for head injuries) are caused by falls, 10% by assaults, 16.5% by being struck or against something, 17% by motor vehicle accidents, 21% by other/unknown ways. In addition, the highest rate of injury is among children ages 0–14 and adults age 65 and older.

The main treatment for isolated epispadias is a comprehensive surgical repair of the genito-urinary area usually during the first 7 years of life, including reconstruction of the urethra, closure of the penile shaft and mobilisation of the corpora. The most popular and successful technique is known as the modified Cantwell-Ransley approach. In recent decades however increasing success has been achieved with the complete penile disassembly technique despite its association with greater and more serious risk of damage.