Tobacco smoking is associated with an increased risk of ureteral cancer.

The main medical risk factors are having bladder cancer or having conditions that cause chronic inflammation in the urethra. People over the age of 60 and white women have the highest risks.

Between 1988 and 2001 in the United States, cancer surveillance reports to SEER included 1,333 cases of ureteral cancer in adults: 808 male and 525 female, 1,158 white and 42 black. Of the total, 1,251 (94%) were transitional cell carcinoma of the papillary type. "Five-year relative survival rates from cancers of the ureter were similar among males vs. females..."

Studies indicate that dietary patterns may affect development of BPH, but further research is needed to clarify any important relationship. Studies from China suggest that greater protein intake may be a factor in development of BPH. Men older than 60 in rural areas had very low rates of clinical BPH, while men living in cities and consuming more animal protein had a higher incidence. On the other hand, a study in Japanese-American men in Hawaii found a strong negative association with alcohol intake, but a weak positive association with beef intake. In a large prospective cohort study in the US (the Health Professionals Follow-up Study), investigators reported modest associations between BPH (men with strong symptoms of BPH or surgically confirmed BPH) and total energy and protein, but not fat intake. There is also epidemiological evidence linking BPH with metabolic syndrome (concurrent obesity, impaired glucose metabolism and diabetes, high triglyceride levels, high levels of low-density cholesterol, and hypertension).

Prognosis can range considerably for patients, depending where on the scale they have been staged. Generally speaking, the earlier the cancer is diagnosed, the better the prognosis. The overall 5-year survival rate for all stages of penile cancer is about 50%.

It is also known that disruption of the endocrine system by certain chemicals adversely affects the development of the reproductive system and can cause vaginal cancer. Many other reproductive diseases have also been link to exposure to synthetic and environmental chemicals. Common chemicals with known links to reproductive disorders include: lead, dioxins and dioxin-like compounds, styrene, toluene, BPA (Bisphenol A) and pesticides.

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.

Most experts consider androgens (testosterone and related hormones) to play a permissive role in the development of BPH. This means that androgens must be present for BPH to occur, but do not necessarily directly cause the condition. This is supported by evidence suggesting that castrated boys do not develop BPH when they age. In an unusual study of 26 eunuchs from the palace of the Qing dynasty still living in Beijing in 1960, the prostate could not be felt in 81% of the studied eunuchs. The average time since castration was 54 years (range, 41–65 years). On the other hand, some studies suggest that administering exogenous testosterone is not associated with a significant increase in the risk of BPH symptoms, so the role of testosterone in prostate cancer and BPH is still unclear. Further randomized controlled trials with more participants are needed to quantify any risk of giving exogenous testosterone.

Dihydrotestosterone (DHT), a metabolite of testosterone, is a critical mediator of prostatic growth. DHT is synthesized in the prostate from circulating testosterone by the action of the enzyme 5α-reductase, type 2. DHT can act in an autocrine fashion on the stromal cells or in paracrine fashion by diffusing into nearby epithelial cells. In both of these cell types, DHT binds to nuclear androgen receptors and signals the transcription of growth factors that are mitogenic to the epithelial and stromal cells. DHT is ten times more potent than testosterone because it dissociates from the androgen receptor more slowly. The importance of DHT in causing nodular hyperplasia is supported by clinical observations in which an inhibitor of 5α-reductase such as finasteride is given to men with this condition. Therapy with a 5α-reductase inhibitor markedly reduces the DHT content of the prostate and, in turn, reduces prostate volume and BPH symptoms.

Testosterone promotes prostate cell proliferation, but relatively low levels of serum testosterone are found in patients with BPH. One small study has shown that medical castration lowers the serum and prostate hormone levels unevenly, having less effect on testosterone and dihydrotestosterone levels in the prostate.

While there is some evidence that estrogen may play a role in the cause of BPH, this effect appears to be mediated mainly through local conversion of androgens to estrogen in the prostate tissue rather than a direct effect of estrogen itself. In canine "in vivo" studies castration, which significantly reduced androgen levels but left estrogen levels unchanged, caused significant atrophy of the prostate. Studies looking for a correlation between prostatic hyperplasia and serum estrogen levels in humans have generally shown none.

In 2008, Gat et al. published evidence that BPH is caused by failure in the spermatic venous drainage system resulting in increased hydrostatic pressure and local testosterone levels elevated more than 100 fold above serum levels. If confirmed, this mechanism explains why serum androgen levels do not seem to correlate with BPH and why giving exogenous testosterone would not make much difference.

Penile cancer is a rare cancer in developed nations with annual incidence varying from 0.3 to 1 per 100,000 per year accounting for around 0.4–0.6% of all malignancies. The annual incidence is approximately 1 in 100,000 men in the United States, 1 in 250,000 in Australia, and 0.82 per 100,000 in Denmark. In the United Kingdom, fewer than 500 men are diagnosed with penile cancer every year.

However, in the developing world penile cancer is much more common. For instance, in Paraguay, Uruguay, Uganda and Brazil the incidence is 4.2, 4.4, 2.8 and 1.5–3.7 per 100,000, respectively. In some South American countries, Africa, and Asia, this cancer type constitutes up to 10% of malignant diseases in men.

The lifetime risk has been estimated as 1 in 1,437 in the United States and 1 in 1,694 in Denmark.

Examples of congenital abnormalities of the reproductive system include:

- Kallmann syndrome - Genetic disorder causing decreased functioning of the sex hormone-producing glands caused by a deficiency or both testes from the scrotum.

- Androgen insensitivity syndrome - A genetic disorder causing people who are genetically male (i.e. XY chromosome pair) to develop sexually as a female due to an inability to utilize androgen.

- Intersexuality - A person who has genitalia and/or other sexual traits which are not clearly male or female.

Frisch & Simonsen (2016) carried out a very large scale study in Denmark, which compared the incidence of meatal stenosis in Muslim males (mostly circumcised) with the incidence of meatal stenosis in ethnic Danish males (mostly non-circumcised). The risk of meatal stenosis in circumcised males was found to be as much 3.7 times higher than in the intact, non-circumcised males.

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.

Urethral diverticulum can occur in men, and can cause complications including kidney stones and urinary tract infections.

The incidence of urethral diverticulum has been increasing in the 2000s, likely due to increasing diagnosis and detection of the condition. It is estimated to be present in as low as 0.02% of all women and as high as 6% of all women, and 40% of women with lower urinary tract symptoms. Most symptomatic urethral diverticula are present in women from 30–60 years old.

84% of periurethral masses are due to urethral diverticula.

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

Lymphoma is the most common type of blood-related cancer in horses and while it can affect horses of all ages, it typically occurs in horses aged 4–11 years.

Links between maternal smoking and TDS are tenuous, but there are stronger associations between maternal alcohol consumption and incidences of cryptorchidism in sons. Smoking does however affect the growth of a fetus, and low birth weight is shown to increase the likelihood of all the disorders encompassed by TDS. Maternal obesity, resulting in gestational diabetes, has also been shown to be a risk factor for impaired testes development and TDS symptoms in sons.

It is a rare condition, with only approximately 60 cases reported as of 1989, and 75 cases as of 2005. However, due to the stigma of intersex conditions and the issues of keeping accurate statistics and records among doctors, it is likely there are more cases than reported.

Poor semen quality is measured not only by the number of sperm a man produces but also by how effective the sperm is at fertilising an egg. The motility and shape of the sperm are important for this role. A man with poor semen quality will often present with fertility problems which is defined as a couple trying to conceive for over 1 year with no success. Diagnosis can be made from semen analysis, taking a sample of the man’s semen and running tests to count numbers and quality of the individual sperm.

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.

Numerous studies over a long period of time clearly indicate that male circumcision contributes to the development of urethral stricture. Among circumcised males, reported incidence of meatal stricture varies. Griffiths "et al". (1985) reported an incidence of 2.8 percent. Sörensen & Sörensen (1988) reported 0 percent. Cathcart "et al". (2006) reported an incidence of 0.55 percent. Yegane "et al". (2006) reported an incidence of 0.9 percent. Van Howe (2006) reported an incidence of 7.29 percent. In Van Howe's study, all cases of meatal stenosis were among circumcised boys. Simforoosh "et al". (2010) reported an incidence of 0.55 percent. According to Emedicine (2016), the incidence of meatal stenosis runs from 9 to 20 percent. Frisch & Simonsen (2016) placed the incidence at 5 to 20 percent of circumcised boys.

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.

Post-void dribbling or post-micturition dribbling is the where urine remaining in the urethra after voiding the bladder slowly leaks out after urination. A common and usually benign complaint, it may be a symptom of urethral diverticulum, prostatitis and other medical problems.

Men who experience dribbling, especially after prostate cancer surgery, will choose to wear incontinence pads to stay dry. Also known as guards for men, these incontinence pads conform to the male body. Some of the most popular male guards are from Tena, Depends, and Prevail. Simple ways to prevent dribbling include: strengthening pelvic muscles with Kegel exercises, changing position while urinating, or pressing on the perineum to evacuate the remaining urine from the urethra. Sitting down while urinating is also shown to alleviate complaints: a meta-analysis on the effects of voiding position in elderly males with benign prostate hyperplasia found an improvement of urologic parameters in this position, while in healthy males no such influence was found.

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.

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.