Chlamydia trachomatis (genital) diagnosis and management

Last updated: June 2013


Nucleic Acid Amplification Test

Note: NAAT refers to Nucleic Acid Amplification Test, such as PCR

Diagnosis is made on a positive sample from an infected site such as:

  • first catch urine or urethral swab in males
  • physician collected or self-collected vaginal swab
  • endocervical swab
  • physician collected or self collected rectal swab in males and females
  • in females without a cervix or in whom swabs cannot be taken, a first catch urine is tested
  • conjunctiva
  • Nasopharynx in infants at risk of neonatal transmission.

Note: Women should be asked about anal sex and appropriately tested. 


Serology is of no value in the diagnosis of genital tract chlamydial infection.

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Standard therapy for oropharyngeal, urethral, endocervical, conjunctival sites

Azithromycin 1 g orally as one dose (B1)


Doxycycline 100 mgs orally twice a day for 10 days (D).


Azithromycin 1 g orally as one dose (B1)


Amoxycillin 500 mgs orally tds for seven days (A).

Standard therapy for rectal site

Doxycycline 100 mg orally twice a day for 10 days (D).

Rectal site in pregnancy

Azithromycin 1 g weekly for two doses (B1).

Epidemiologic treatment

Epidemiologic treatment is given to sexual partners, regardless of age or gender, of persons with chlamydia.

All contacts should have appropriate investigations for chlamydia before treatment is provided.


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Contact tracing

Patients should be encouraged to contact all sexual partners in the last six months for testing and treatment.

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Patient education

The following points should be discussed:

  • chlamydia is sexually transmitted
  • chlamydia is a common infection
  • infection is asymptomatic in up to 50% of men and 90% of women
  • re-infection may occur during or after treatment
  • abstinence from sex (including oral sex) until 1 week after patient and partner treatment
  • chlamydia is a notifiable disease
  • advise on the side effects of medications
  • a test of cure is required at six weeks
  • discuss window periods for other STI and HIV
  • reinforce safe sex.

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Follow up

  • clinical review 1 week after treatment for symptomatic patients
  • test of cure is required at 6 weeks
  • assess medication compliance if single dose therapy not used
  • check if the patient experienced any reactions to the medication
  • enquire about further sexual activity since diagnosis, reinforce prevention and safe sex practices
  • confirm contact tracing
  • screen for Human Immunodeficiency Virus (HIV) and syphilis at 3 months.

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Further information

For further information on the diagnosis and management of genital chlamydia trachomatis contact Clinic 275.

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These guidelines are based on review of current literature, current recommendations of the United States Centers for Disease Control and Prevention, World Health Organization, the British Association for Sexual Health and HIV and local expert opinion.

They are written primarily for use by Clinic 275 staff and some flexibility is required in applying them to certain private practice situations.

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