Should a patient with a history of anal warts and autoimmune disorders receive the human papillomavirus (HPV) vaccine, such as Gardasil 9 (recombinant human papillomavirus 9-valent vaccine), to prevent future infections and reduce the risk of developing anal cancer?

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HPV Vaccination After Anal Warts

Yes, patients with a history of anal warts should receive the HPV vaccine (Gardasil 9) regardless of prior HPV infection, as vaccination is recommended irrespective of history of genital warts and can prevent future infections with other HPV types not yet acquired. 1

Primary Recommendation

The Advisory Committee on Immunization Practices (ACIP) explicitly states that vaccination should be given irrespective of history of abnormal Pap, HPV, or genital warts. 1 This is a critical point—prior HPV infection or manifestation of disease (such as anal warts) does not contraindicate vaccination and should not delay it.

Age-Based Vaccination Guidelines

For Patients Through Age 26

  • Routine vaccination is recommended for all individuals through age 26 who have not completed the vaccine series 1
  • Men who have sex with men (MSM), people living with HIV, and immunocompromised persons should be vaccinated through age 26 years 1
  • The 9-valent HPV vaccine (Gardasil 9) is the preferred formulation, protecting against HPV types 6,11,16,18,31,33,45,52, and 58 1, 2

For Patients Ages 27-45

  • The FDA expanded Gardasil 9 approval to include individuals aged 27 through 45 years in 2018 1
  • ACIP recommends vaccination based on shared clinical decision-making for individuals in this age range who are not adequately vaccinated 1
  • For patients with anal warts in this age group, vaccination is particularly justified given the high recurrence rates (25-75% at 6 months to 1 year) and the vaccine's ability to prevent infection with HPV types not yet acquired 1

Rationale for Vaccination After Anal Warts

Protection Against Additional HPV Types

  • Anal warts are typically caused by HPV types 6 and 11 3, 2
  • Having warts from HPV 6/11 does not mean the patient has been exposed to high-risk oncogenic types (16,18,31,33,45,52,58) that cause anal cancer 1, 2
  • The 9-valent vaccine protects against 9 HPV types, and prior infection with one type does not confer immunity to others 2, 4

Cancer Prevention Benefits

  • HPV is associated with approximately 90% of anal squamous cell cancers 3, 5
  • The quadrivalent HPV vaccine demonstrated 77.5% efficacy in preventing high-grade anal intraepithelial neoplasia (AIN grades 2-3) in the per-protocol population of MSM 1, 6
  • Real-world data shows that HPV vaccination at younger ages reduces the risk of anal high-grade squamous intraepithelial lesion (HSIL) or worse by 70% (HR = 0.30,95% CI = 0.10 to 0.87) 7
  • The 9-valent vaccine is predicted to prevent an additional 464 cases of anal cancer annually compared to the quadrivalent vaccine 1

Recurrence Prevention

  • Treatment of anal warts has high recurrence rates (25-75% at 6 months to 1 year) 1
  • Vaccination may help reduce recurrence risk by preventing reinfection with vaccine-type HPV strains 8

Special Considerations for Autoimmune Disorders

Safety Profile

  • The HPV vaccine is NOT a live vaccine—it consists of virus-like particles based on the L1 capsid protein 1
  • Individuals receiving the vaccine are not at risk for developing viral infection, even in the setting of underlying immunocompromise 1
  • No serious adverse events directly linked to HPV vaccine administration have been reported in immunocompromised populations 1
  • The most common side effect is headache (up to 50% of patients), with risk of syncope requiring 15-minute observation post-vaccination 1, 2

Efficacy in Immunocompromised Patients

  • Studies in people living with HIV showed the vaccine was immunogenic, with seropositivity rates at month 7 of 98.9% for HPV-6,100% for HPV-11,99.6% for HPV-16, and 97.4% for HPV-18 1
  • For patients with autoimmune disorders on immunosuppressive therapy, vaccination is still recommended, though immune response may be somewhat reduced 1
  • The vaccine should ideally be administered when the patient's immune status is optimized (if on immunosuppressive therapy, consider timing when disease is controlled) 1

Dosing Schedule

Standard 3-Dose Regimen (Ages 15-45)

  • 0,2, and 6 months 2
  • Each dose is 0.5 mL administered intramuscularly in the deltoid region 2

2-Dose Regimen (Ages 9-14 Only)

  • 0 and 6-12 months (not applicable for most adults with anal warts) 2

Key Clinical Pitfalls to Avoid

  1. Do not delay vaccination because the patient has already had anal warts—this is explicitly NOT a contraindication 1
  2. Do not assume the patient has been exposed to all vaccine-type HPV strains simply because they have had warts 2
  3. Do not withhold vaccination in patients with autoimmune disorders—the vaccine is not live and is safe in immunocompromised individuals 1
  4. Observe patients for 15 minutes post-vaccination due to syncope risk 2
  5. Counsel patients that vaccination does not eliminate the need for continued anal cancer screening if it has been recommended by their healthcare provider 2
  6. The vaccine is not a treatment for existing anal warts or precancerous lesions—it prevents future infections 2

Contraindications

The only absolute contraindications are:

  • Hypersensitivity to yeast (a vaccine component) 2
  • Severe allergic reaction after a previous dose of Gardasil 9 or Gardasil 2

Autoimmune disorders are NOT listed as contraindications in the FDA label 2.

References

Guideline

Guideline Directed Topic Overview

Dr.Oracle Medical Advisory Board & Editors, 2025

Guideline

HPV Effects in Men

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Guideline

Clearance of Anal HPV in Men Who Have Sex with Men

Praxis Medical Insights: Practical Summaries of Clinical Guidelines, 2025

Research

Prophylactic HPV vaccination and anal cancer.

Human vaccines & immunotherapeutics, 2016

Professional Medical Disclaimer

This information is intended for healthcare professionals. Any medical decision-making should rely on clinical judgment and independently verified information. The content provided herein does not replace professional discretion and should be considered supplementary to established clinical guidelines. Healthcare providers should verify all information against primary literature and current practice standards before application in patient care. Dr.Oracle assumes no liability for clinical decisions based on this content.

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