Chlamydia infections are usually asymptomatic in both men and women. Infection in men can cause urethritis with discharge and dysuria and can lead to epididymo-orchitis. In women infection can cause cervicitis with vaginal discharge and post coital bleeding. Complications in women include pelvic inflammatory disease (PID), ectopic pregnancy and infertility. Mother-to-child transmission can lead to neonatal conjunctivitis and pneumonitis.


Nucleic acid amplification testing (NAAT) for chlamydia using PCR or strand displacement assay is highly sensitive and specific for C. trachomatis. However, false positive results do occur and should be considered in low risk individuals where a positive result was unexpected.


Sexually active women aged 25 and under should be offered screening for chlamydia opportunistically. Using NAAT, women, can be tested for chlamydia using an endocervical swab, first void urine or a vaginal swab. Self taken vaginal swabs are as sensitive as clinician taken and are acceptable to many women. Urine may not be as sensitive as a vaginal swab but may be most appropriate in a reluctant patient.

Women screened for chlamydia who have a positive result should be asked about symptoms of PID including pelvic pain, deep dyspareunia and intermenstrual bleeding. If there are symptoms and signs of PID then treatment for PID should be given. Please see treatment guidelines on PID


Men at risk for infection should be opportunistically screened. Men can be screened for urethral chlamydia using a first void urine specimen for NAAT.

Men who have sex with men should be screened for urethral, pharyngeal and rectal chlamydia at least once a year or as risks dictates in addition to other infections.  An anal swab for chlamydia NAAT is used to screen men who have sex with men for rectal chlamydia and self collected swabs are as sensitive as clinician taken and may be preferred by some men. 

For the investigation of men who present with symptoms of urethral or rectal infection, refer to the MSHC treatment guidelines on urethritis and proctitis.

If a chlamydia result is equivocal or inhibitors are present the test should be repeated. If the initial test was a urine sample, the repeat test should be performed using a swab. 


Uncomplicated genital and pharyngeal infection in men and women 

  • Azithromycin 1 gram as a single dose or
  • Doxycycline 100mg twice daily for 7 days 
Chlamydia rectal infection

The treatment of non-LGV rectal chlamydia is currently controversial with some evidence that single dose azithromycin may not be as effective as doxycycline. However randomized evidence for this is lacking. Men who have sex with men who are screened for rectal chlamydia and who have a positive result should be asked carefully about symptoms of proctitis: anorectal pain and discharge. If no symptoms of proctitis treat with:

  • Azithromycin 1 gram as a single dose  or Doxy 100mg bd for 7 days

For rectal chlamydia with symptoms of proctitis consider rectal LGV and treat with:

  • Doxycycline 100mg orally twice daily for 21 days  

See MSHC treatment guideline on LGV.

Chlamydia epididymo-orchitis:
  • Azithromycin 1 gram as a single dose plus
  • Doxycycline 100mg twice daily for 14 days
Chlamydia PID

Refer to MSHC treatment guideline on PID

Chlamydia in pregnant women


  • Azithromycin 1 gram as a single dose


  • Amoxycillin 500mg three times daily for 7 days or 
  • Erythromycin ethylsuccinate (EES) 800mg four times daily for 7 days or 
  • Erythromycin ethylsuccinate (EES) 400mg four times daily for 14 days


For genital and pharyngeal chlamydia (male and female) a repeat chlamydia test to exclude re-infection is recommended at three months as re-infection rates are high. Repeating a test to ensure cure for chlamydia is not recommended except in pregnant women where it should be performed because of low efficacy of some antibiotics. 

For rectal chlamydia infections, whether LGV or otherwise, a repeat anal swab should be performed at one month after commencing treatment as a test of cure.

If a repeat test following treatment is performed it should not be done within 4 weeks of commencing treatment as a persistently positive result could reflect detection of non viable DNA. 


Partner notification should be discussed with patients diagnosed with chlamydia as sex with untreated chlamydia infected partners can result in repeat infection. Consider referring patients to the Let Them Know website (   which is designed to support patients to undertake partner notification and which facilitates sending of SMS and email messages to partners. Partners should be contacted, tested and treated without waiting for their test results. Individuals should abstain from sex with their partners until 7 days after both have received treatment.


Chlamydia is notifiable to the Victorian Health Department by doctors and laboratories and a notification form should be completed.

The content of these treatment guidelines is for information purposes only. The treatment guidelines are generic in character and should be applied to individuals only as deemed appropriate by the treating practitioner on a case by case basis. Alfred Health, through MSHC, does not accept liability to any person for the information or advice (or the use of such information or advice) which is provided through these treatment guidelines. The information contained within these treatment guidelines is provided on the basis that all persons accessing the treatment guidelines undertake responsibility for assessing the relevance and accuracy of the content and its suitability for a particular patient. Responsible use of these guidelines requires that the prescriber is familiar with contraindications and precautions relevant to the various pharmaceutical agents recommended herein.

Last Updated January 2017