Patient Population: Pediatric

This and other STI sections are not meant to be comprehensive references for all STI treatment but primarily focused on the most commonly used initial empiric antimicrobial therapy. Users should refer to linked resources (SFDPH City Clinic protocols, CDC guidelines) or other local resources to provide patients and their partners appropriate counseling and follow-up. For non-adolescent age patients, patients with STIs not addressed in these guidelines, or patients with contraindications to the listed therapies, we recommend referring to the linked resources, or Lexi-Comp for medication information, or consulting ID/ASP for individualized recommendations.   

Condition Major Pathogens  First Choice Therapy Alternative Therapy Comments

Chlamydia (uncomplicated anogenital tract infection) 

See Pelvic Inflammatory Disease section for patients with consistent clinical findings

Chlamydia trachomatis  Doxycycline
100 mg enterally bid 

If pregnancy has not been excluded, or anticipate significant challenges to adherence:  

1000 mg enterally x 1 dose* 

*Doxycycline is likely superior to azithromycin for treatment of chlamydia in all sites, and particularly for rectal and urethral chlamydia 

All sexual partners within preceding 60 days should be notified, tested, and treated; if not feasible then expedited partner therapy is recommended 

Refer to SFDPH City Clinic STI protocols section on chlamydia for recommended laboratory evaluation (including testing for other STIs), and further recommendations on partner treatment, counseling (including abstinence from sex during patient and partner treatment), and follow up (including retesting in 3 months) 

Duration: 7 days for doxycycline, single dose for azithromycin 


Workowski KA, et al. Centers for Disease Control and Prevention. Sexually transmitted infections treatment guidelines, 2021. MMWR Recomm Rep 2021;70:1-187.

St. Cyr S, et al. Update to CDC’s treatment guidelines for gonococcal infection, 2020. MMWR Morb Mortal Wkly Rep 2020;69:1911–1916.

San Francisco Department of Public Health City Clinic New Guidelines for Treatment of Gonococcal Infection, 12/2020 

Kong FYS, et al. Azithromycin versus doxycycline for the treatment of genital chlamydia infection: a meta-analysis of randomized controlled trials. Clin Infect Dis 2014;59:193–205.

Dombrowski JC et al, Doxycycline versus azithromycin for the treatment of rectal chlamydia in men who have sex with men: a randomized controlled trial. Clin Infect Dis, 2021 (epub)

Dukers-Muijrers N, et al. Treatment effectiveness of azithromycin and doxycycline in uncomplicated rectal and vaginal Chlamydia trachomatis infections in women: a multicenter observational study (FemCure). Clin Infect Dis, 2019; 69: 1946-1954 

Chandra NL, et al.  Detection of Chlamydia trachomatis in rectal specimens in women and its association with anal intercourse: a systematic review and meta-analysis. Sex Transm Infect 2018; 94:320–6.

Jensen JS, et al. Azithromycin treatment failure in Mycoplasma genitalium-positive patients with nongonococcal urethritis is associated with induced macrolide resistance. Clin Infect Dis. 2008;47:1546–53. 

Bachmann LH, et al. Measured versus self-reported compliance with doxycycline therapy for chlamydia-associated syndromes: high therapeutic success rates despite poor compliance. Sex Transm Dis. 1999; 26:272-278.

Pediatric Empiric Antimicrobial Therapy Guidelines

This is a subsection of the UCSF Benioff Children’s Hospitals Empiric Antimicrobial Therapy Guidelines, developed by the Pediatric Antimicrobial Stewardship Programs at each campus to inform initial selection of empiric antimicrobial therapy for children at the UCSF Benioff Children’s Hospitals and affiliated outpatient sites. 

These are guidelines only and not intended to replace clinical judgment. Modification of therapy may be indicated based on patient comorbidities, previous antibiotic therapy or infection history. Doses provided are usual doses but may require modification based on patient age or comorbid conditions. Refer to Pediatric Antimicrobial Dosing Guideline for further guidance on dosing in children, and Neonatal Dosing Guideline for infants < 1 month of age. Consult a pediatric pharmacist for individualized renal or hepatic dose adjustment. Durations provided are usual recommendations for patients who are responding appropriately to therapy. For additional guidance, please contact Pediatric Infectious Diseases (ID) or the Pediatric Antimicrobial Stewardship Program (ASP) at the campus where your patient is receiving care.  

For questions or feedback about these guidelines, please email primary content owners, Rachel Wattier, Pediatric ASP Medical Director at BCH SF and Prachi Singh, Pediatric ASP Medical Director at BCH OAK. 

The content of these guidelines was updated in July 2021. See Summary and Rationale for Changes (password login to Box needed) for detailed explanations of the content changes.