• The most commonly reported communicable disease in Australia
  • Those <30 years are at greatest risk
  • Frequently asymptomatic
  • Simple to test and treat
  • Immunity to new infection is not provided by previous infection.


Chlamydia trachomatis (See also Lymphogranuloma venereum).

Clinical presentation

Male Female

50% have no symptoms

75% have no symptoms



Urethral discharge

 Vaginal discharge

Testicular pain

 Pelvic pain

Ano-rectal symptoms 

 Intermenstrual bleeding


 Postcoital bleeding


Ano-rectal symptoms

Epididymo-orchitis Pelvic inflammatory disease (PID)
Reactive arthritis: arthralgia, hypertrophic rash on soles, circinate balanitis, psoriatic rash Infertility
  Ectopic pregnancy
  Reactive arthritis: arthralgia, hypertrophic rash on soles, psoriatic rash

See STI Atlas for images.

Special considerations

May also infect the eye, anus and rarely throat.


Diagnosis in males
NAAT First Pass Urine (FPU)

If MSM also collect anal and pharyngeal swab even if asymptomatic at these sites.

NAAT Ano-rectal swab If MSM, and patient declines anal examination or has no ano-rectal symptoms, instruct in
If ano-rectal symptoms present, collect via proctoscope, or encourage
self-collection rectal swab.
NAAT Pharyngeal swab Collect if MSM.
NAAT – Nucleic Acid Amplification Test 
FPU – First pass urine 
MSM – Men who have sex with men


Diagnosis in females
NAAT Endocervical swab Best test if examined
NAAT Self-collected vaginal swab If not examined
NAAT FPU Only if endocervical swab/self-collected vaginal swab cannot be taken e.g. after a hysterectomy. Not as sensitive as self-collected vaginal swab.
NAAT Ano-rectal swab If patient has had anal sex or has ano-rectal symptoms.
If patient declines anal examination, instruct
self-collection or refer patient for testing to sexual health centre.
NAAT – Nucleic Acid Amplification Test
FPU – First pass urine

Specimen collection

Clinician collected |

Asymptomatic patients can collect most samples themselves, including vaginal swabs and ano-rectal swabs.


  • NAATs are highly sensitive, and can be used in non clinical and non urban settings. They are the only easily accessible tests for chlamydia.
  • Encourage patient self-collection of vaginal swabs, urine and ano-rectal swabs. 
  • Gonorrhoea can and should be tested for on the same NAAT specimens.

Clinical indicators for testing

Test for chlamydia in the following situations:

  • <30 years and sexually active
  • partner change in the last 12 months
  • have had an STI in past 12 months
  • have had a sexual partner with an STI
  • at increased risk of complications of an STI e.g. termination of pregnancy (TOP) or intrauterine device (IUD) insertion
  • signs or symptoms suggestive of chlamydia
  • patient requests a sexual health check.


Principal Treatment Options
Uncomplicated genital or pharyngeal infection

Doxycycline 100mg PO, BD 7 days


Azithromycin 1g PO, stat


Ano-rectal infection

Doxycycline 100mg PO, BD 7 days if asymptomatic, but 21 days if symptomatic (see ano-rectal syndromes)

Azithromycin 1g PO, stat, and repeat in 1 week

Treatment advice

  • Treat immediately if high index of suspicion. If urethritis symptoms use Doxycycline while awaiting test results (See NSU) or if contact of index case use either Azithromycin or Doxycycline depending on assessment of adherence or patient preference
  • Start treatment for patient and sexual partner(s) without waiting for lab results.
  • Use azithromycin as the principle treatment option when nursing administered standing orders available.
  • If a patient has an intrauterine device (IUD), leave IUD in place and treat as recommended. Seek specialist advice as needed.
  • If symptomatic anorectal infection, ensure lymphogranuloma venereum (LGV) testing is requested.

Other immediate management

  • Advise no sexual contact for 7 days after treatment is administered.
  • Advise no sex with partners from the last 6 months until the partners have been tested and treated if necessary.
  • Contact tracing.
  • Provide patient with factsheet.
  • Notify the state/territory health department.

Special treatment situations

Special considerations

  • Consider seeking specialist advice before treating any complicated presentation.
Pregnant women 
Azithromycin 1g PO, stat
Allergy to principal treatment choice

If both principle treatment options unsuitable, seek specialist advice.

Rectal coinfection

For rectal coinfection with gonorrhoea, treatment should be given for both infections i.e.:

Ceftriaxone 500mg IMI, stat in 2mL 1% lignocaine


Doxycycline 100mg PO, BD 7 days if asymptomatic, but 21 days if symptomatic (see ano-rectal syndromes)

Contact tracing

  • Contact tracing is important to prevent reinfection and reduce transmission
  • Male and female partners should be traced back for 6 months
  • Offer recommended treatment to all sexual contacts
  • Consider the use of patient delivered partner therapy (PDPT), where appropriate. PDPT is currently legal in VIC and NT.

See Australasian Contract Tracing Manual - Chlamydia for more information.

Follow up

Review in 1 week provides an opportunity to:

  • Confirm patient adherence with treatment and assess for symptom resolution.
  • Confirm contact tracing procedures have been undertaken or offer more contact tracing support.
  • Provide further sexual health education and prevention counselling.

Test of Cure (TOC)

Not routinely recommended, unless in the following groups:

  • Pregnant women
  • Rectal chlamydia

TOC by Nucleic Acid Amplification Test (NAAT) in these situations should be performed at least 4 weeks after treatment is completed. An earlier TOC could yield a false positive result due to the presence of chlamydia DNA remnants.


  • Re-infection is common
  • Re-testing at 3 months is recommended, to detect re-infection.

Consider testing for other STIs, if not undertaken at first presentation, or retesting post the window period.

Auditable outcomes

  • 100% of patients diagnosed with chlamydia are treated with an appropriate antibiotic regimen
  • 100% of patients are advised to avoid sexual contact for 7 days after treatment is administered
  • 50% of patients are retested at 3 months.
Last Updated: Thursday, 29 March 2018