A vaginal yeast infection results from overgrowth of candida albicans, or yeast, in the vagina. This is a relatively common infection, with over 75% of women having experienced at least one yeast infection at some point in their life. Risk factors for yeast infections include recent antibiotic use, diabetes, immunosuppression, increased estrogen levels, and use of certain contraceptive devices including intrauterine devices, diaphragms, or sponges. It is not a sexually transmitted infection. Candida vaginal infections are common; an estimated 75% of women will have at least one yeast infection in their lifetime. Vaginal discharge is not always present in yeast infections, but when occurring it is typically odorless, thick, white, and clumpy. Vaginal itching is the most common symptom of candida vulvovaginitis. Women may also experience burning, soreness, irritation, pain during urination, or pain during sex. The diagnosis of Candida vulvovaginitis is made by looking at a sample taken from the vagina under the microscope that shows hyphae (yeast), or from a culture. It is important to note that the symptoms described above may be present in other vaginal infections, so microscopic diagnosis or culture is needed to confirm the diagnosis. Treatment is with intra-vaginal or oral anti-fungal medications.

Bacterial vaginosis (BV) is an infection caused by a change in the vaginal flora, which refers to the community of organisms that live in the vagina. It is the most common cause of pathological vaginal discharge in women of childbearing age and accounts for 40–50% of cases. In BV, the vagina experiences a decrease in a bacterium called lactobacilli, and a relative increase in a multitude of anaerobic bacteria with the most predominant being "Gardnerella vaginalis". This imbalance results in the characteristic vaginal discharge experienced by patients with BV. The discharge in BV has a characteristic strong fishy odor, which is caused by the relative increase in anaerobic bacteria.[1] The discharge is typically thin and grey, or occasionally green. It sometimes is accompanied by burning with urination. Itching is rare. The exact reasons for the disruption of vaginal flora leading to BV are not fully known. However, factors associated with BV include antibiotic use, unprotected sex, douching, and using an intrauterine device (IUD). The role of sex in BV is unknown, and BV is not considered an STI. The diagnosis of BV is made by a health care provider based on the appearance of the discharge, discharge pH > 4.5, presence of clue cells under the microscope, and a characteristic fishy odor when the discharge is placed on a slide and combined with potassium hydroxide ("whiff test"). The gold standard for diagnosis is a gram stain showing a relative lack of lactobacilli and a polymicrobial array of gram negative rods, gram variable rods, and cocci. BV may be treated with oral or intravaginal antibiotics, or oral or intravaginal lactobacillus.

Penile discharge is fluid that comes from the urethra at the end of the penis. This may occur with infections due to gonorrhea, chlamydia, or trichomoniasis. In gonorrhea the discharge may by white, yellow, or green.

Although previously considered a mere nuisance infection, untreated bacterial vaginosis may cause complications, such as increased susceptibility to sexually transmitted infections including HIV and pregnancy complications.

It has been shown that HIV-infected women with bacterial vaginosis (BV) are more likely to transmit HIV to their sexual partners than those without BV. Diagnostic criteria for BV have also been associated with a female genital tract factor that induces expression of HIV.

There is evidence of an association between BV and increased rates of sexually transmitted infections such as HIV/AIDS. BV is associated with up to a six-fold increase in HIV shedding. There is also a correlation between the absence of vaginal lactobacilli and infection by Neisseria gonorrhea and Chlamydia trachomatis. BV is a risk factor for viral shedding and herpes simplex virus type 2 infection. BV may increase the risk of infection with or reactivation of human papillomavirus (HPV).

In addition, bacterial vaginosis an intercurrent disease in pregnancy may increase the risk of pregnancy complications, most notably premature birth or miscarriage.

Pregnant women with BV have a higher risk of chorioamnionitis, miscarriage, preterm birth, premature rupture of membranes, and postpartum endometritis. BV is associated with gynecological and obstetric complications. Data suggest an association between BV, tubal factor infertility, and pelvic inflammatory disease. Women with BV who are treated with in vitro fertilization have a lower implantation rate and higher rates of early pregnancy loss.

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.

Hormonal vaginitis includes atrophic vaginitis usually found in postmenopausal or postpartum women. Sometimes it can occur in young girls before puberty. In these situations the estrogen support of the vagina is poor.

Healthy vaginal microbiota consists of species which neither cause symptoms or infections, nor negatively affect pregnancy. It is dominated mainly by Lactobacillus species. BV is defined by the disequilibrium in the vaginal microbiota, with decline in the number of lactobacilli. While the infection involves a number of bacteria, it is believed that most infections start with Gardnerella vaginalis creating a biofilm, which allows other opportunistic bacteria to thrive.

One of the main risks for developing BV is douching, which alters the vaginal flora and predisposes women to developing BV. Douching is strongly discouraged by the U.S. Department of Health and Human Services and various medical authorities, for this and other reasons.

BV is a risk factor for pelvic inflammatory disease, HIV, sexually transmitted infections (STIs), and reproductive and obstetric disorders or negative outcomes. It is possible for sexually inactive persons to develop bacterial vaginosis.

Bacterial vaginosis may sometimes affect women after menopause. Also, subclinical iron deficiency may correlate with bacterial vaginosis in early pregnancy. A longitudinal study published in February 2006, in the "American Journal of Obstetrics and Gynecology", showed a link between psychosocial stress and bacterial vaginosis persisted even when other risk factors were taken into account. Exposure to the spermicide nonoxynol-9 does not affect the risk of developing bacterial vaginosis.

Having a female partner increases the risk of BV by 60%. The bacteria associated with BV have been isolated from male genitalia. BV microbiota has been found in the penis, coronal sulcus, and male urethra, in the male partners of infected females. Partners who have not been circumcised may act as a ‘reservoir’ increasing the likelihood of acquiring an infection after sexual intercourse. Another mode of transmission of the BV-associated microbiota is to a female sexual partner via skin-to-skin transfer. BV may be transmitted via the perineal enteric bacteria from the microbiota of the female and male genitalia.

Vaginitis is the disruption of the healthy vaginal microbiota. The vaginal microbiota consists of those organisms which generally do not cause symptoms, infections, and results in good pregnancy outcomes, and is dominated mainly by Lactobacillus species. The disruption of the normal microbiota can cause a vaginal yeast infection. Vaginal yeast infection can affect women of all ages and is very common. The yeast "Candida albicans" is the most common cause of vaginitis. Specific forms of vaginal inflammation include the following types:

Infectious vaginitis accounts for 90% of all cases in reproductive age women:

- Candidiasis: vaginitis caused by proliferation of "Candida albicans", "Candida tropicalis", "Candida krusei"

- Bacterial vaginosis: vaginitis caused by increased growth of "Gardnerella" (a bacterium).

- Aerobic vaginitis

Other less common infections are caused by gonorrhea, chlamydia, "Mycoplasma", herpes, "Campylobacter", improper hygiene, and some parasites, notably "Trichomonas vaginalis". Women who have diabetes develop infectious vaginitis more often than women who do not.

Vaginal infections often have multiple causes (varies between countries between 20 and 40% of vaginal infections), which present challenging cases for treatment. Indeed, when only one cause is treated, the other pathogens can become resistant to treatment and induce relapses and recurrences. Therefore, the key factor is to get a precise diagnosis and treat with broad spectrum anti-infective agents (often also inducing adverse effects).

Further, either a change in pH balance or introduction of foreign bacteria in the vagina can lead to infectious vaginitis. Physical factors that have been claimed to contribute to the development of infections include the following: constantly wet vulva due to tight clothing, chemicals coming in contact with the vagina via scented tampons, antibiotics, birth control pills, or a diet favoring refined sugar and yeast.

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.

Research has shown a link between trichomoniasis and two serious sequelae. Data suggest that:

- Trichomoniasis is associated with increased risk of transmission and infection of HIV.

- Trichomoniasis may cause a woman to deliver a low-birth-weight or premature infant.

- The role of trichomonas infection in causing cervical cancer is unclear, although trichomonas infection may be associated with co-infection with high-risk strains of HPV.

- "T. vaginalis" infection in males has been found to cause asymptomatic urethritis and prostatitis. In the prostate, it may create chronic inflammation that may eventually lead to prostate cancer.

It is not a major issue but is to be resolved as soon as possible. It can be a natural defense mechanism that the vagina uses to maintain its chemical balance, as well as to preserve the flexibility of the vaginal tissue. The term "physiologic leukorrhea" is used to refer to leukorrhea due to estrogen stimulation.

Leukorrhea may occur normally during pregnancy. This is caused by increased bloodflow to the vagina due to increased estrogen. Female infants may have leukorrhea for a short time after birth due to their in-uterine exposure to estrogen.

Leukorrhea is also caused by trichomonads, a group of parasitic protozoan, specifically "Trichomonas vaginalis". Common symptoms of this disease are burning sensation, itching and discharge of frothy substance, thick, white or yellow mucous.

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 most common bacterial cause of NGU is "Chlamydia trachomatis", but it can also be caused by "Ureaplasma urealyticum", "Haemophilus vaginalis", "Mycoplasma genitalium", Mycoplasma hominis, Gardnerella vaginalis, Acinetobacter lwoffi, Ac.calcoclaceticus and "E.coli".

There are many causes of NGU. This is in part due to the large variety of organisms living in the urinary tract. "Ureaplasma urealyticum" and "Mycoplasma genitalium" are some of the culprits.

NGU is also associated with Reiter's syndrome,in which triad of Arthritis,Conjunctivitis & Urethritis is there.

There were about 58 million cases of trichomoniasis in 2013. It is more common in women (2.7%) than males (1.4%). It is the most common non-viral STI in the U.S., with an estimated 3.7 million prevalent cases and 1.1 million new cases per year. It is estimated that 3% of the general U.S. population is infected, and 7.5-32% of moderate-to-high risk (including incarcerated) populations.

Balanitis "is a common condition affecting 11% of adult men seen in urology clinics and 3% of children" in the United States; globally, balanitis "may occur in up to 3% of uncircumcised males".

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.

Gonorrhea if left untreated may last for weeks or months with higher risks of complications. One of the complications of gonorrhea is systemic dissemination resulting in skin pustules or petechia, septic arthritis, meningitis, or endocarditis. This occurs in between 0.6 and 3% of infected women and 0.4 and 0.7% of infected men.

In men, inflammation of the epididymis, prostate gland, and urethra can result from untreated gonorrhea. In women, the most common result of untreated gonorrhea is pelvic inflammatory disease. Other complications include inflammation of the tissue surrounding the liver, a rare complication associated with Fitz-Hugh–Curtis syndrome; septic arthritis in the fingers, wrists, toes, and ankles; septic abortion; chorioamnionitis during pregnancy; neonatal or adult blindness from conjunctivitis; and infertility. Men who have had a gonorrhea infection have an increased risk of getting prostate cancer.

Newborn babies coming through the birth canal are given erythromycin ointment in the eyes to prevent blindness from infection. The underlying gonorrhea should be treated; if this is done then usually a good prognosis will follow. Adults may also have eyes infected with gonorrhoea and require proper personal hygiene and medications.

Among persons in the United States between 14 and 39 years of age, 46% of people with gonorrheal infection also have chlamydial infection.

The infection is usually spread from one person to another through vaginal, oral, or anal sex. Men have a 20% risk of getting the infection from a single act of vaginal intercourse with an infected woman. The risk for men that have sex with men (MSM) is higher. Active MSM may get a penile infection, while passive MSM may get anorectal gonorrhea. Women have a 60–80% risk of getting the infection from a single act of vaginal intercourse with an infected man. A pregnant women can pass on the infection to her unborn infant.

A mother may transmit gonorrhea to her newborn during childbirth; when affecting the infant's eyes, it is referred to as ophthalmia neonatorum. It may be able to spread through the objects contaminated with body fluid from an infected person. The bacteria typically does not survive long outside the body, typically dying within minutes to hours.

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

A genital ulcer is located on the genital area, usually caused by a sexually transmitted disease such as genital herpes, syphilis, chancroid, or "Chlamydia trachomatis". Some other signs of having genital ulcers include enlarged lymph nodes in the groin area, or vesicular lesions, which are small, elevated sores or blisters. The syndrome may be further classified into penile ulceration and vulval ulceration for males and females respectively.

Genital ulcers are not strictly a sign of an STD. They can occur in patients with Behcet's syndrome, lupus, and some forms of rheumatoid arthritis (all non-communicable diseases). Genital tuberculosis, often caused by direct genital contact with infected sputum, can also present as genital ulcer.

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.

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.

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.