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 2-60 days or longer. 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 75% of women and 50% 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.
  • Abnormal bleeding (intermenstrual, post coital bleeding) due to cervicitis.
  • Lower abdominal pain due to pelvic inflammatory disease (PID), or infection of the fallopian tubes or uterus
  • Dyspareunia (pain during vaginal intercourse)
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 7 to 14 days, but may be longer.

Testing should be carried out on sexual partners of infected individuals, and should be considered for sexually active adolescent girls and boys. Consider testing 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.

STI Atlas (external site)


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). 
  • In women who decline to be examined or it is not indicated, self-obtained vaginal swabs are the preferred specimen.
  • If the patient is examined take an endocervical swab for NAAT (no transport medium) in addition to FVU testing. A urine specimen only, is acceptable if a woman declines to give either a vaginal or endocervical swab, but will miss some cervical infections. 
  • 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.
  • Gonorrhoea can and should be tested for on the same NAAT specimens.

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 urethral swab can be used if the patient prefers not to wait.
  • Women: Take a FVU and endocervical swab or SOLVS for NAAT (no transport medium).
  • 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.

NB -FVU is first void urine - meaning collecting the first part of the urine stream, it can be done at any time and does not have to be the first void of the day. 

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

  • If the patient has had receptive anal sex, oro-anal sex, rimming or fingering, and no anal symptoms: patients can be instructed how to take two blind anal swabs himself or herself. Refer to the STI self-testing card (PDF 346KB) for instructions.
  • If the patient has had receptive oral sex and no oral symptoms, take a throat swab for NAAT (no transport medium). 

Treating uncomplicated chlamydia


  • Doxycycline 100 mg orally, 12-hourly for 7 days This is the preferred treatment as it reduces opportunities for M. genitalium to develop resistance to azithromycin and is effective against asymptomatic rectal carriage of C. trachomatis


  • Azithromycin 1 g orally, as a single dose

Where there is any concern that the patient will not be compliant with doxycycline, azithromycin may be more suitable.

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, twice daily for 7 days.

Pregnant women

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


  • Erythromycin ethyl succinate 800 mg orally, twice daily for 10 days (category A)


  • Erythromycin base 250 mg orally, 6-hourly for 14 days (category A)

See Australian categorisation system for prescribing medicines in pregnancy (external site)

Ano-rectal infection

  • Doxycyline 100mg orally, twice daily for 7 days; if LGV detected treat for 21 days if symptomatic


  • Azithromycin 1g orally, as a single dose, and repeat in one week

For treatment of adults and mature minors (aged 14 years or older) with chlamydia under a Structured Administration and Supply Arrangement, see Structured Administration and Supply Arrangement - CEO of Health SASA. This is suitable for use by Registered Nurses and Aboriginal Health Practitioners employed by a health service operated or managed by a Health Service Provider of the WA Department of Health, or contracted entity.

Pharyngeal infection

  • Azithromycin 1g orally as single dose (same as for lower genital infections) 

Advise patients no sexual contact for 7 days after the treatment is administered. 

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.

For further information see Australian categorisation system for prescribing medicines in pregnancy (external site).

For provision of free treatment for chlamydia, see the Structured Administration and Supply Arrangement - WA Country Health Nurses (PDF 140KB) and the Structured Administration and Supply Arrangement – WA Health Aboriginal Health Practitioners (PDF 140KB)

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, early miscarriage, post-partum PID, 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. 

For treatment of adults and mature minors (aged 14 years or older) with chlamydia under a Structured Administration and Supply Arrangement, see Structured Administration and Supply Arrangement - CEO of Health SASA. This is suitable for use by Registered Nurses and Aboriginal Health Practitioners employed by a health service operated or managed by a Health Service Provider of the WA Department of Health, or contracted entity.

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 or doxycycline 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. 

Reasonable steps should be made to review patients three months after exposure as this provides an opportunity to test for reinfection and repeat blood tests for syphilis, HIV and HBV.

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.

Epidemiological reports and real time notification data