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Chlamydial and Other Nongonococcal Infections


Sheldon R. Morris

, MD, MPH, University of California San Diego

Last full review/revision Jan 2021| Content last modified Jan 2021
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Topic Resources

Chlamydial infections include sexually transmitted diseases of the urethra, cervix, and rectum that are caused by the bacteria Chlamydia trachomatis. These bacteria can also infect the membranes that cover the whites of the eyes (conjunctiva) and the throat. Other bacteria, such as Ureaplasma and Mycoplasma, can also cause infections of the urethra.

  • Symptoms include a discharge from the penis or vagina and painful or more frequent urination.

  • If unnoticed or untreated in women, these infections can result in infertility, miscarriage, and an increased risk of a mislocated (ectopic) pregnancy.

  • DNA tests of a sample of the discharge or of urine can detect chlamydial infection.

  • Antibiotics can cure the infection, and sex partners should be treated at the same time.

Several bacteria, including Chlamydia trachomatis (chlamydiae), Ureaplasma, and Mycoplasma, cause similar diseases, all of which resemble the sexually transmitted disease (STD) gonorrhea. Laboratories can identify chlamydiae but have difficulty identifying the other bacteria, so these are sometimes called nongonococcal infections.

Chlamydial infection is the most commonly reported STD. In the United States, over 1.8 million cases were reported in 2018. Because the infection frequently causes no symptoms, twice as many people than are reported to have chlamydial infection may actually be infected.

Chlamydial infection and gonorrhea cause similar symptoms. Both can cause urethral infections (urethritis) in men and, in women, cervical infections (cervicitis) that produce pus (see also Chlamydial Infections and Mycoplasmas).

Sometimes people have gonorrhea and chlamydial infection at the same time.


In men, symptoms of chlamydial urethritis start 7 to 28 days after the infection is acquired during intercourse. Typically, men feel a mild burning sensation in their urethra during urination and may have a clear or cloudy discharge from the penis. The discharge is usually less thick than the discharge in gonorrhea. The discharge may be small, and symptoms mild. However, early in the morning, the opening of the penis is often red and stuck together with dried secretions. Occasionally, the infection begins more dramatically—with a frequent urge to urinate, painful urination, and a discharge of pus from the urethra.

Many women with chlamydial cervicitis have few or no symptoms. But some have frequent urges to urinate, painful urination, and a discharge of yellow mucus and pus from the vagina. Sexual intercourse may be painful.

If the rectum is infected, people may have rectal pain or tenderness and a yellow discharge of pus and mucus from the rectum.

Chlamydial infection can also be spread during oral sex, causing infection of the throat. Chlamydial throat infection usually causes no symptoms.

Without treatment, symptoms lessen within 4 weeks in about two thirds of people. However, chlamydial infections can have serious long-term consequences for women, even when their symptoms are mild or absent. Thus, detecting the infection in women and treating them is important, even if symptoms are absent.

Did You Know...

  • Chlamydial infections are the most common sexually transmitted disease.


In women, complications from chlamydial infection include

  • Scarring of the fallopian tubes

  • Infection of the fallopian tubes (salpingitis)

  • Infection of the membrane that lines the pelvis and abdominal cavity (peritonitis)

  • Infection in the area around the liver

The infection may spread up the reproductive tract and may infect the tubes that connect the ovaries to the uterus (fallopian tubes). This infection, called salpingitis, causes severe lower abdominal pain. In some women, the infection spreads to the lining of the pelvis and abdominal cavity (peritoneum), causing peritonitis. Peritonitis causes more severe pain in the lower abdomen. These infections are considered pelvic inflammatory disease. Sometimes infection concentrates in the area around the liver, in the upper right part of the abdomen, causing pain, fever, and vomiting—called the Fitz-Hugh-Curtis syndrome.

Complications include chronic abdominal pain and scarring of the fallopian tubes. The scarring can cause infertility and mislocated (ectopic) pregnancies.

In men, complications from chlamydial infection include

  • Infection of the epididymis

  • Narrowing (stricture) of the urethra

Chlamydial infections may cause infection of the epididymis (epididymitis). The epididymis is the coiled tube on top of each testis (see figure Pathway From the Penis to the Epididymis). This infection causes painful swelling of the scrotum on one or both sides. The infection may lead to narrowing of the urine passage through the penis (urethra) due to scarring.

Pathway From the Penis to the Epididymis

Occasionally in men, organisms spread up the urethra and travel through the tube that carries sperm from the testis (vas deferens) to infect the epididymis at the top of a testis.

Pathway From the Penis to the Epididymis

In either sex, complications from chlamydial infection include

  • Infection of the membrane that covers the white of the eye (conjunctivitis)

  • Reactive arthritis

Chlamydial genital infections occasionally cause a joint inflammation called reactive arthritis (previously called Reiter syndrome). Reactive arthritis typically affects only one or a few joints at once. The knees and other leg joints are affected most often. The inflammation seems to be an immune reaction to the genital infection rather than spread of the infection to the joints. Symptoms typically begin 1 to 3 weeks after the initial chlamydial infection. Reactive arthritis sometimes is associated with other problems, such as changes in the skin of the feet, problems with the eyes, and inflammation of the urethra.

In newborns, complications from chlamydial infection include

  • Conjunctivitis

  • Pneumonia

Newborns may be infected with Chlamydia during delivery if their mother has a chlamydial infection of the cervix. In newborns, the infection may result in pneumonia or conjunctivitis (neonatal conjunctivitis).


  • Usually tests on a sample of discharge from the cervix, penis, throat, or rectum or a sample of urine

Doctors suspect chlamydial, ureaplasmal, and mycoplasmal infections based on symptoms, such as a discharge from the penis or cervix.

In most cases, doctors diagnose chlamydial infections by doing tests that detect the bacteria’s unique genetic material (DNA). Usually, a sample of the discharge from the penis or cervix is used. Sometimes women are asked to use a swab to obtain a sample from their vagina. For some types of these tests, a urine sample can be used. If a urine sample can be used, people can avoid the discomfort of having a swab inserted into the penis or having a pelvic examination to obtain a sample.

If doctors suspect infection of the throat or rectum, samples from those sites may be tested.

Gonorrhea, which is often also present, can be diagnosed using the same sample. Blood tests to check for human immunodeficiency virus (HIV) infection and syphilis are usually also done.


Because chlamydial infection is so common and because many infected women have no symptoms, tests to screen for chlamydial infection and other STDs are recommended for certain sexually active women and men.

Women who are not pregnant (including women who have sex with women) are screened annually if they have characteristics that increase their risk of infection:

  • Sexually active and under age 25

  • A previous STD

  • Participation in risky sexual activities (such as having many sex partners, not using condoms regularly, or participating in sex work)

  • A partner who participates in risky sexual activities or has an STD

Pregnant women are screened during their initial prenatal visit. The following pregnant women are screened again during the 3rd trimester:

  • All who are under age 25

  • Those who are age 25 and older if their risk of infection is increased

If pregnant women have a chlamydial infection, they are treated. These women are tested again within 3 months.

Heterosexually active men are not routinely screened except if their risk of chlamydial infection is increased—for example, when they have several sex partners, when they are patients at an adolescent or STD clinic, or when they are admitted into a correctional facility.

Men who have sex with men are screened as follows:

  • If they are sexually active: At least once a year

  • If they are at increased risk (those with HIV infection, multiple sex partners, or a partner who has multiple partners): Every 3 to 6 months

These men are screened whether they use condoms or not. Tests are done using samples taken from the rectum, the urethra, or, if they engaged in oral sex, the throat.


The following general measures can help prevent chlamydial infections (and other STDs):

  • Avoidance of unsafe sex practices, such as frequently changing sex partners or having sexual intercourse with prostitutes or with partners who have other sex partners

  • Prompt diagnosis and treatment of the infection (to prevent spread to other people)

  • Identification of the sexual contacts of infected people, followed by counseling or treatment of these contacts

Not having sex (anal, vaginal, or oral) is the most reliable way to prevent STDs but is often unrealistic.


  • An antibiotic

  • Simultaneous treatment of sex partners

Chlamydial, ureaplasmal, and mycoplasmal infections are treated with one of the following antibiotics:

  • A single dose of the antibiotic azithromycin taken by mouth

  • Doxycycline, erythromycin, levofloxacin, or ofloxacin taken by mouth for 7 days

Pregnant women are treated with azithromycin.

If gonorrhea is possible, an antibiotic such as ceftriaxone, injected into a muscle, is given at the same time to treat gonorrhea. Such treatment is needed because the symptoms of the two infections are similar and because many people have both infections at the same time.

Symptoms may persist or return for one of the following reasons:

  • Other infections that are also present may be causing the symptoms.

  • People may have become infected again.

  • The chlamydiae may be resistant to antibiotics.

In such cases, tests for chlamydial infection and gonorrhea are repeated, and sometimes tests for other infections are done. Then people are treated with azithromycin or, if azithromycin was used before and was ineffective, with moxifloxacin.

Sex partners should be treated simultaneously if possible. Infected people and their sex partners should abstain from sexual intercourse until they have been treated for at least 1 week.

The risk of another chlamydial infection or another STD within 3 to 4 months is high enough that people should be tested again at that time.

More Information

The following English-language resource may be useful. Please note that THE MANUAL is not responsible for the content of this resource.

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