Genital chlamydia infection is caused by some of the subtypes of Chlamydia trachomatis. Other subtypes cause trachoma and lymphogranuloma venereum (LGV). Like all chlamydial species, the organism has to grow within cells, and so it is found within the endothelium and epithelium of the endocervix, rectum, peritoneal cavity, fallopian tubes, oropharynx and conjunctiva. Genital chlamydia is a common STI in Australia, particularly in adolescents and young adults.

The incubation period is 7-14 days or longer. The period of communicability is unknown but relapses are probably common. Contact infectivity is high with 68% of male partners of infected women found positive by NAAT (PCR)

Clinical presentation

Asymptomatic infection is common. Chlamydia is asymptomatic in at least 60 per cent of women and 25 per cent of men.

Genital chlamydia infection may be manifested by:

  • urethral discharge (typically clear, white or grey) in men
  • testicular or scrotal pain and tenderness due to epididymo-orchitis
  • vaginal discharge or abnormal bleeding due to cervicitis
  • abdominal pain and fever due to pelvic inflammatory disease (PID), or infection of the fallopian tubes or uterus
  • infertility or ectopic pregnancy due to previous PID, which may or may not have been symptomatic. Patients may have persisting chlamydia infection
  • dysuria (pain on passing urine)
  • and less commonly as:
    • peri-hepatitis (abdominal pain, fever, tender liver)
    • conjunctivitis in adults or newborns
    • proctitis (anal irritation and discharge)
    • pneumonia of newborns
    • reactive arthritis (Reiter's syndrome).

The incubation period for symptomatic urethritis in men is about seven to 14 days, but may be longer.

Screening should be carried out on asymptomatic partners of infected individuals, and should be considered for sexually active adolescent girls and young women at the time of gynaecological examination, even in the absence of symptoms. The highest risk is in those who do not consistently use barrier contraceptives, or who have a new partner or multiple partners.


Chlamydia infection is diagnosed by detecting Chlamydia trachomatis in appropriate specimens. Serology is not helpful in the diagnosis of sexually transmitted chlamydial infection.

  • The preferred tests are nucleic acid amplification tests (NAAT). Culture is now used only in special circumstances.
  • In women who decline to be examined or it is not indicated, self-obtained vaginal swabs are the preferred specimen. Add a first void urine (FVU) specimen where possible. If the patient is examined take a endocervical swab only. A urine specimen only, is acceptable if a woman declines to give either a vaginal or endocervical swab.
  • Diagnosis and treatment of infected patients prevents ongoing/further transmission to sex partners and, for infected pregnant women, may prevent transmission of chlamydia to infants during birth.

Specimen collection and handling

  • Men: Collect FVU for NAAT. If the patient is unable to pass urine, ask him to wait or provide the patient with a specimen jar and ask him to return a FVU at his earliest convenience. A urethral swab could be used if the patient prefers not to wait.
  • Women: Take an endocervical swab or cytobrush or SOLVS or FVU for NAAT. The handling of the swab or cytobrush depends on the test used. Follow the instructions provided by the laboratory.
  • Specimens should reach the laboratory as quickly as possible.
  • All specimens must be clearly labelled with the patient's identifier (name or code), date of birth or medical record number, the site, date and time of collection.
  • Keep as close as possible to 4 °C during storage and transport. Avoid extremes of temperature. Do not place samples in the freezer section of the refrigerator and avoid direct contact with freezer blocks during transport.

See further information on methods of testing, including use of GeneXpert point-of-care test in health services where this is available.


Directly observed single dose therapy is preferred.

Treating uncomplicated chlamydia


  • Azithromycin 1 g orally, as a single dose (preferred treatment)


  • doxycycline 100 mg orally, 12-hourly for 7 days

Children 0–8 years

  • Azithromycin 10 mg/kg (to a maximum of 1 g) orally, daily for 5 days (restricted PBS availability)


  • erythromycin 10 mg/kg per day orally, in four doses for 10–14 days.

Children > 8 years

  • Azithromycin 20 mg/kg (to a maximum of 1 g) orally, as a single dose


  • doxycycline 100 mg orally, 12-hourly for 7 days.

Pregnant women

  • Azithromycin 1 g orally, as a single dose (category B1) (preferred option)


  • erythromycin ethyl succinate 800 mg orally, 12-hourly for 10 days (category A)


Special considerations

Tetracycline antibiotics, including doxycycline, should never be used in:

  • women who are pregnant or possibly pregnant, or breastfeeding
  • children under nine years old.

Erythromycin estolate is contraindicated in pregnancy due to increased risk of hepatotoxicity.

Treating chlamydia in cases of gonorrhoea

Many patients with gonorrhoea will also have chlamydia, although the converse is less likely.

Presumptive treatment of chlamydia in patients being treated for gonorrhoea may be appropriate, especially in highly endemic areas.

See gonorrhoea.

Treating chlamydia in cases of Pelvic inflammatory disease (PID)

See PID.

Treating chlamydia in cases of epididymitis/epididymo-orchitis

See epididymitis/epididymo-orchitis.

Treating chlamydia in cases of Lymphogranuloma venereum (LVG)

See LGV.

Related links

Education counselling and prevention

Counselling is important in managing STIs/HIV and should be considered at every contact with the patient. As a minimum, consider counselling at the first presentation, and subsequently during treatment and follow-up.

  • Counselling is an opportunity to educate and support the patient in prevention strategies. This should be done in a confidential setting.
  • The key points are:
    • communicating the confidentiality of the diagnosis
    • communicating the reasons for testing and contact tracing
    • formulating expectations from treatment
    • promoting awareness of risk behaviours.
  • Counselling should also include discussion of the implications of STI testing (i.e. that testing does not prevent transmission). Emotional reactions can accompany a positive STI/HIV diagnosis with delayed reactions sometimes occurring several days after the consultation. 
Management of partners

It is the responsibility of all health care providers, including doctors, to begin tracing sex partners so that they can be assessed and treated.

This involves counselling to ensure that the patient understands the implications of infection transmission.

Managing sex partners may require referral to another practitioner.

  • Contact tracing in cases of chlamydia infection is important. Untreated chlamydia can lead to PID, infertility, ectopic pregnancy, chronic pelvic infection, neonatal pneumonia, pre-term delivery and neonatal conjunctivitis.
  • The duration of potential infectivity may be months to years.
  • All sex partners of the index case from the preceding six months should be tested, where practical. In circumstances where testing is not possible, consider treatment for both chlamydia and gonorrhoea. If the history of the index case suggests they are likely to have been infectious for longer than six months, then reasonable efforts should be made to screen earlier contacts.
  • Transmission of chlamydia by oral sex is low. 
Follow up

To ensure continuity of care, record follow-up instructions in the patient's medical record.

Consider the need to review symptomatic patients in approximately one week. This is an opportunity for further education and counselling.

As NAAT can remain positive for three to four weeks after treatment, repeat sampling to exclude re-infection should be undertaken if possible at least one month after treatment in the following circumstances:

  • where regimens other than azithromycin are used
  • in children
  • in pregnant women
  • where there is doubt about compliance with treatment and advice
  • where symptoms persist
  • where there appear to be complicated infections such as PID or epididymitis
  • where there is a high risk of re-infection. 
Public health issues

Contact tracing is important to prevent further transmission and reinfection. Always test for other STIs.

If a child is diagnosed with genital chlamydia, issues of sexual abuse and/or sexual assault should be considered and mandatory notification of infection forwarded to the local PHU. For further information, see Child sexual abuse and STIs.


This is a notifiable infection. Medical practitioners must complete the appropriate notification forms for all patients diagnosed with a notifiable STI/HIV, as soon as possible after confirmed diagnosis.