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Chlamydia: The Basics

Chlamydia: The Basics
Two 100 mg doxycycline tablets, the preferred treatment for chlamydia 


Chlamydia is the second most common sexually transmitted infection (STI) in the United States.  More than 1.8 million chlamydia cases were reported in 2019, though the actual number of infections was much higher, since many more cases go undiagnosed and unreported.  Young adults ages 20-24 have the highest rates of chlamydia in the United States.

Chlamydia usually causes no symptoms.  However, left untreated, it can lead to serious long-term complications.  The good news is, chlamydia is easy to treat when detected.

What is Chlamydia?

Chlamydia is a bacterial infection caused by Chlamydia trachomatis. It is primarily transmitted through sexual contact and can infect the genital tract of men and women, as well as the mouth and anus.  Immunity to infection is not long-lived, and as a result, reinfection or persistent infection is common.

Risk of Infection

Anyone having vaginal, oral, or anal sex can become infected.  General features associated with a higher likelihood of getting chlamydia include:

  • Being a sexually active adolescent or young adult
  • Having a new sex partner or more than one sex partner
  • Having a history of a prior STI, including chlamydia
  • Inconsistent condom use

Chlamydia Symptoms

Chlamydia can cause mild to severe symptoms in some cases, but most people experience no symptoms at all.  This makes it easy to spread chlamydia without knowing.

Women can get chlamydia in the cervix (part of the lower genital tract), rectum and/or throat.  When symptoms do occur, they most commonly include:

  • Unusual discharge from your vagina
  • Discomfort when you urinate or when you have sex
  • Irritation or itching around your genitals
  • Pelvic pain
  • Abnormal vaginal bleeding

Men can get chlamydia in the urethra, rectum or throat. Often, there are no symptoms.  When symptoms do occur, the can include:

  • Penis discharge
  • Pain with urination
  • Testicular pain and tenderness

Chlamydia can also cause conjunctivitis (eye infection) when exposed to infected fluids like vaginal discharge or semen.  In rare cases, infection causes a several symptoms collectively known as reactive arthritis that include joint pain, uveitis (inflammation of the inner part of the eye) and pain with urination.

Complications from Chlamydia

Left untreated, C. trachomatis can ascend into the upper genital tract in women, infecting the uterus, fallopian tubes, and ovaries and causing pelvic inflammatory disease (PID). Symptoms of PID include abdominal and pelvic pain, cervical motion tenderness, fevers and can lead to infertility, ectopic pregnancy, and chronic pelvic pain.(1)

Chlamydia can also put anyone at a higher risk of getting HIV (the virus that causes AIDS), especially if your sexual partner is HIV-positive.

Incubation Period

The incubation period of symptomatic disease ranges from 5 to 14 days after infection.  Untreated, there is the possibility of spontaneous clearing of infection, (2) however all persons diagnosed should be treated to avoid complications and transmission.  Once established but undetected, modeling studies suggest an untreated chlamydial infection duration of almost 3 years in males and 1.35 years in females.(3)

Detecting Chlamydia and Screening

Testing for chlamydia is done with a urine sample or from a rectal or oral swab.

The Center for Disease Control (CDC) and Prevention recommends that women be tested at least once a year who are:

  • Younger than 25 and sexually active
  • 25 or older with several sexual partners
  • 25 or older with a new sexual partner
  • Pregnant

The CDC also recommends that men be tested at least once a year who are:

  • Having sex with other men (gay or bisexual)

Any sexual active individual with signs and symptoms consistent with chlamydial infection should undergoing testing.

We also think it reasonable to screen heterosexual males who have a history of STI or are seeking STI evaluation.


The goals of treatment are (a) to prevent complicated infections related to chlamydia, (b) decrease the transmission to others, (c) resolve symptoms - the vast majority of symptomatic patients improve clinically within two weeks of treatment, and (d) prevent reinfection.

Doxycycline is the preferred antibiotic to treat C. trachomatis infection in non-pregnant individuals;(4) the recommended dose is 100 mg twice a day for seven days.  Previously, single-dose azithromycin was the preferred option, but the evidence suggests doxycycline is superior, especially for rectal and oral infection.(5)

Mediation adherence is extremely important.  One study defined imperfect adherence to a week-long course of oral doxycycline as missing one or more doses and found a marked ninefold risk of microbiologic failure among males with urethral chlamydia.(6)

Chlamydia Prevention

Wait To prevent reinfection, everyone who tests positive for chlamydia should be treated and abstain from sexual intercourse until they and their partner(s) can complete treatment.

Outreach If you test positive for chlamydia, we recommend contacting all sexual partners you had in the last 60 days so that they can be screened and treated for chlamydia and other STIs.  If you haven’t and sexual contact within anyone in the last 60 days, then we recommend reaching out to the last person you had sex with.

Retest We follow the CDC recommendations and encourage all patients with a documented chlamydial infection to retest three months after treatment, since reinfection rates are high.

Testing to assess whether treatment eradicated the infection (test for cure) is recommended in a limited number of settings:

  • If you’re regnant
  • If your symptoms do not improve after treatment
  • If you did not complete the recommended treatment

Mona can assist you with with retesting, outreach, and test for cure.


  1. Tubal infertility: serologic relationship to past chlamydial and gonococcal infection. World Health Organization Task Force on the Prevention and Management of Infertility. Sex Transm Dis. 1995 Mar-Apr;22(2):71-7. PMID: 7624815.
  2. Geisler WM, Lensing SY, Press CG, Hook EW 3rd. Spontaneous resolution of genital Chlamydia trachomatis infection in women and protection from reinfection. J Infect Dis. 2013 Jun 15;207(12):1850-6. doi: 10.1093/infdis/jit094. Epub 2013 Mar 7. PMID: 23470847; PMCID: PMC3654745.
  3. Lewis J, Price MJ, Horner PJ, White PJ. Genital Chlamydia trachomatis Infections Clear More Slowly in Men Than Women, but Are Less Likely to Become Established. J Infect Dis. 2017 Jul 15;216(2):237-244. doi: 10.1093/infdis/jix283. Erratum in: J Infect Dis. 2018 Jan 17;217(3):511. PMID: 28838150; PMCID: PMC5854005.
  4. Workowski KA, Bachmann LH, Chan PA, Johnston CM, Muzny CA, Park I, Reno H, Zenilman JM, Bolan GA. Sexually Transmitted Infections Treatment Guidelines, 2021. MMWR Recomm Rep. 2021 Jul 23;70(4):1-187. doi: 10.15585/mmwr.rr7004a1. PMID: 34292926; PMCID: PMC8344968.
  5. Kong FY, Tabrizi SN, Law M, Vodstrcil LA, Chen M, Fairley CK, Guy R, Bradshaw C, Hocking JS. Azithromycin versus doxycycline for the treatment of genital chlamydia infection: a meta-analysis of randomized controlled trials. Clin Infect Dis. 2014 Jul 15;59(2):193-205. doi: 10.1093/cid/ciu220. Epub 2014 Apr 11. PMID: 24729507.
  6. Khosropour CM, Manhart LE, Colombara DV, Gillespie CW, Lowens MS, Totten PA, Golden MR, Simoni J. Suboptimal adherence to doxycycline and treatment outcomes among men with non-gonococcal urethritis: a prospective cohort study. Sex Transm Infect. 2014 Feb;90(1):3-7. doi: 10.1136/sextrans-2013-051174. Epub 2013 Oct 8. PMID: 24106340; PMCID: PMC4057099.