Symptoms that may be caused by urethral cancer include:

Bleeding from the urethra or blood in the urine,

Weak or interrupted flow of urine,

Urination occurs often, painful urination, inability to pass urine,

A lump or thickness in the perineum or penis,

Discharge from the urethra,

Enlarged lymph nodes or pain in the groin or vaginal area.

Symptoms of ureteral cancer may include "blood in the urine (hematuria); diminished urine stream and straining to void (caused by urethral stricture); frequent urination and increased nighttime urination (nocturia); hardening of tissue in the perineum, labia, or penis; itching; incontinence; pain during or after sexual intercourse (dyspareunia); painful urination (dysuria); recurrent urinary tract infection; urethral discharge and swelling".

Urethral cancer is cancer originating from the urethra. Cancer in this location is rare, and the most common type is papillary transitional cell carcinoma. The most common site of urethral cancer is the bulbomembranous urethra.

Ureteral cancer is cancer of the ureters, muscular tubes that propel urine from the kidneys to the urinary bladder. It is also known as ureter cancer, renal pelvic cancer, and rarely ureteric cancer or uretal cancer. Cancer in this location is rare.

Ureteral cancer is usually transitional cell carcinoma. Transitional cell carcinoma is "a common cause of ureter cancer and other urinary (renal pelvic) tract cancers."

Penile cancer is a malignant growth found on the skin or in the tissues of the penis. Around 95% of penile cancers are squamous cell carcinomas. Other types of penile cancer such as Merkel cell carcinoma, small cell carcinoma, melanoma and other are generally rare.

Penile cancer arises from precursor lesions, which generally progress from low-grade to high-grade lesions. For HPV related penile cancers this sequence is as follows:

- A. Squamous hyperplasia;

- B. Low-grade penile intraepithelial neoplasia (PIN);

- C. High-grade PIN (carcinoma in situ—Bowen's disease, Erythroplasia of Queyrat and bowenoid papulosis (BP));

- D. Invasive Carcinoma of the Penis.

However, in some cases non-dysplastic or mildly dysplastic lesions may progress directly into cancer. Examples include flat penile lesions (FPL) and condylomata acuminata.

In HPV negative cancers the most common precursor lesion is lichen sclerosus (LS).

BPH is the most common cause of lower urinary tract symptoms (LUTS), which are divided into storage, voiding, and symptoms which occur after urination. Storage symptoms include the need to urinate frequently, waking at night to urinate, urgency (compelling need to void that cannot be deferred), involuntary urination, including involuntary urination at night, or urge incontinence (urine leak following a strong sudden need to urinate). Voiding symptoms include urinary hesitancy (a delay between trying to urinate and the flow actually beginning), intermittency (not continuous), involuntary interruption of voiding, weak urinary stream, straining to void, a sensation of incomplete emptying, and terminal dribbling (uncontrollable leaking after the end of urination, also called post-micturition dribbling). These symptoms may be accompanied by bladder pain or pain while urinating, called dysuria.

Bladder outlet obstruction (BOO) can be caused by BPH. Symptoms are abdominal pain, a continuous feeling of a full bladder, frequent urination, acute urinary retention (inability to urinate), pain during urination (dysuria), problems starting urination (urinary hesitancy), slow urine flow, starting and stopping (urinary intermittency), and nocturia.

BPH can be a progressive disease, especially if left untreated. Incomplete voiding results in residual urine or urinary stasis, which can lead to an increased risk of urinary tract infection.

Anterior urethral cancer is a disease in which malignant cancer cells are found in the part of the urethra that is closest to the outside of the body.

Benign prostatic hyperplasia (BPH), also called prostate enlargement, is a noncancerous increase in size of the prostate. Symptoms may include frequent urination, trouble starting to urinate, weak stream, inability to urinate, or loss of bladder control. Complications can include urinary tract infections, bladder stones, and chronic kidney problems.

The cause is unclear. Risk factors include a family history, obesity, type 2 diabetes, not enough exercise, and erectile dysfunction. Medications like pseudoephedrine, anticholinergics, and calcium channel blockers may worsen symptoms. The underlying mechanism involves the prostate pressing on the urethra thereby making it difficult to pass urine out of the bladder. Diagnosis is typically based on symptoms and examination after ruling out other possible causes.

Treatment options including lifestyle changes, medications, a number of procedures, and surgery. In those with mild symptoms weight loss, exercise, and decreasing caffeine intake is recommended. In those with more significant symptoms medications may include alpha blockers such as terazosin or 5α-reductase inhibitors such as finasteride. Surgical removal of part of the prostate may be carried out in those who do not improve with other measures. Alternative medicine such as saw palmetto do not appear to help.

About 105 million people are affected globally. BPH typically begins after the age of 40. Half of males age 50 and over are affected. After the age of 80 about 90% of males are affected. Although prostate specific antigen levels may be elevated in males with BPH, the condition does not increase the risk of prostate cancer.

Examples of functional problems of the reproductive system include:

- Impotence - The inability of a male to produce or maintain an erection.

- Hypogonadism - A lack of function of the gonads, in regards to either hormones or gamete production.

- Ectopic pregnancy - When a fertilized ovum is implanted in any tissue other than the uterine wall.

- Hypoactive sexual desire disorder - A low level of sexual desire and interest.

- Female sexual arousal disorder - A condition of decreased, insufficient, or absent lubrication in females during sexual activity

- Premature ejaculation - A lack of voluntary control over ejaculation.

- Dysmenorrhea - Is a medical condition of pain during menstruation that interferes with daily activities

A Gartner's duct cyst (sometimes incorrectly referred to as "vaginal inclusion cyst") is a benign vaginal cystic lesion that arises from the Gartner's duct, which is a vestigial remnant of the mesonephric duct (wolffian duct) in females. They are typically small asymptomatic cysts that occur along the lateral walls of the vagina, following the course of the duct. They can present in adolescence with painful menstruation (Dysmenorrhea) or difficulty inserting a tampon. They can also enlarge to substantial proportions and be mistaken for urethral diverticulum or other structures.

There is a small association between Gartner's duct cysts and metanephric urinary anomalies, such as ectopic ureter & ipsilateral renal hypoplasia. Because of this, imaging is recommended before excision.

A urethral caruncle is a benign cutaneous condition characterized by distal urethral lesions that are most commonly found in post-menopausal women. They appear red, and can be various sizes. They can have the appearance of a tumor. These epidermal growths are found around the posterior portion of the urethral meatus. They can bleed and occasionally dysuria and dyspareunia. The caruncles can be removed by surgery, electric cauterization and then with suture repair. Pathologiy studies are necessary to distinguish carcinoma of the urethra from urethral caruncles. Caruncles can grow back in some instances. Urethral caruncles can accompany the skin changes related to lowered estrogen levels. They can become a source of chronic hematuria, infection, and urethritis.

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.

Examples of cancers of the reproductive system include:

- Prostate cancer - Cancer of the prostate gland

- Breast cancer - Cancer of the mammary gland.

- Ovarian cancer - Cancer of the ovary.

- Penile cancer - Cancer of the penis.

- Uterine cancer - Cancer of the uterus.

- Testicular cancer - Cancer of the testicle/(plural:testes).

- Cervical Cancer - Cancer of the cervix.

Hypospadias presents as an abnormal location for the end of the urethra which is typically found on the distal end of the penis. It is generally diagnosed at birth from visual confirmation of the hallmark features. As well as an unusual location of the urethra, the prepuce (foreskin) is typically incomplete as well. The abnormal ‘hooded’ prepuce is what often draws attention to the condition but can occur separately to hypospadias.

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 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.

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.

Urethral hypermobility is a condition of the female urethra. It describes the instability of the urethra and can be a cause of urinary incontinence. It is sometimes treated with urethral bulking injections.

Urethral syndrome is characterised by a set of symptoms typically associated with lower urinary tract infection, such as painful urination (dysuria) and frequency. It is a diagnosis of exclusion, made when there is no significant presence of bacteriuria with a conventional pathogen ruling out urinary tract infection, and when cystoscopy shows no inflammation of the bladder, ruling out interstitial cystitis and cystitis cystica. In women, vaginitus should also be ruled out.

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.

In Cryptorchidism a diagnosis is made from a physical examination which is performed when the baby is lacking one or both testes in the dependant portion of the scrotal sac. 70% of cryptorchid testes can be felt and are unable to be pulled into the scrotum or retreats quickly after being pulled into a higher position. In 30% of cases the testes cannot be felt indicating an intra-abdominal location. The risk factors for Cryptorchidism are:

- A family history of the condition

- Low birth weight

- Prematurity

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.