What is the difference between the HPV types that cause warts and those that cause cancer?

HPV has over 200 genotypes. The types that cause genital warts — predominantly HPV 6 and 11 — are called low-risk types because they almost never cause cancer. The types associated with cancer — especially HPV 16 and 18, plus types 31, 33, 45, 52, and 58 — are called high-risk types. They can cause cancer of the cervix, anus, vulva, vagina, penis, and throat without producing any visible warts. This is why cervical screening (looking for high-risk HPV DNA) and HPV vaccination are the key cancer-prevention tools, while treatment of visible warts is a separate issue. The [Gardasil 9 vaccine](https://immunisationhandbook.health.gov.au) protects against both the wart-causing types (6 and 11) and the most important cancer-causing types (16, 18, 31, 33, 45, 52, 58) in a single vaccine.

What treatments are available for genital warts in Australia?

Treatment options fall into patient-applied and clinician-applied categories. Patient-applied: **podophyllotoxin 0.5% paint or 0.15% cream (Wartec)** — applied to external warts twice daily for 3 days, then 4 days off, repeated weekly for up to 6 weeks; not used in pregnancy. **Imiquimod 5% cream (Aldara)** — applied to external warts three nights per week, washed off after 6–10 hours, for up to 16 weeks; it works by activating the immune system at the site. Clinician-applied: **cryotherapy with liquid nitrogen** is the most accessible in-clinic option — the wart is frozen with a brief freeze-thaw cycle, repeated every 1–2 weeks until clearance. Trichloroacetic acid (TCA) is an alternative used in clinic and is safe in pregnancy. Larger or refractory warts may need electrocautery, laser, or surgical excision by a specialist. No treatment cures the underlying HPV infection — the immune system clears the virus over time. Recurrence within 3 months is common even after complete clearance.

I've been vaccinated. Can I still get genital warts?

Yes, though much less commonly. Gardasil 9 provides strong protection against HPV types 6 and 11 (which cause ~90% of warts) when given before any exposure to those types — usually before sexual activity starts. If vaccination occurred after some sexual activity, or after a previous HPV infection with those types, the vaccine protects against types not yet acquired but cannot clear types already present. Australia's post-vaccine data show more than a 90% reduction in genital warts diagnoses among vaccinated cohorts, with a significant herd-protection effect in unvaccinated individuals too. Some warts in vaccinated people are caused by types not covered by the vaccine.

What is the cervical screening self-collection option?

Since July 2022, self-collected vaginal swabs have been a fully equivalent option within the National Cervical Screening Program (NCSP). You take your own vaginal swab — in private, in the GP's room — and it is sent for the same HPV-based test as a clinician-collected sample. Detection rates for high-risk HPV DNA are equivalent between the two methods. Self-collection is particularly valuable for women who have delayed screening due to discomfort, trauma, or difficulty accessing a clinician. Ask your GP for the self-collection kit if you would prefer this option — it does not reduce the quality of your screening result.

Does having a wart diagnosis mean I have to tell my partner?

Genital warts are not formally notifiable to health authorities in Australia, so there is no legal obligation to report. However, sexual partners should be made aware that they may have been exposed to HPV — principally so they can ensure their own cervical screening is up to date and consider HPV vaccination if they are eligible. Treating warts in your partner does not prevent you being re-exposed, because they have likely already been exposed to the same virus. Condoms reduce but do not eliminate HPV transmission — HPV spreads by skin-to-skin contact over a wider area than condoms cover. A wart diagnosis does not necessarily indicate recent infidelity, as HPV can remain dormant for months to years before warts become visible.

Anogenital warts and HPV-related disease

Genital warts and HPV: treatment, Gardasil 9, and cervical screening

By Dr HB Lo, FACRRM Reviewed 31 July 2026 10 min read

Genital warts are the most common viral sexually transmissible infection in Australia, caused by low-risk HPV types 6 and 11. The cancer-driving HPV types — especially 16 and 18 — are separate and do not produce visible warts.

Diagnosis is clinical in most cases. Patient-applied podophyllotoxin or imiquimod and clinician-applied cryotherapy remove visible warts. The immune system clears the underlying HPV infection over time, independent of topical treatment.

Australia's Gardasil 9 vaccine programme and HPV-based cervical screening with self-collection from 2022 have produced dramatic reductions in both genital warts and cervical cancer precursors.

HPV and genital warts — the essentials

Human papillomavirus (HPV) is the most common sexually transmissible viral infection in Australia and worldwide. Over 80% of sexually active people acquire at least one HPV type during their lifetime; the vast majority clear it within 1–2 years without any treatment or awareness that infection occurred.

Genital warts are caused by HPV types 6 and 11 — low-risk types. They are highly visible and often distressing to the person affected, but they are not pre-cancerous. The cancer-causing (high-risk) HPV types — especially 16 and 18 — are a completely different matter. They cause cancer of the cervix, anus, vulva, vagina, penis, and throat by silently altering cells over many years, without producing warts. This distinction is fundamental to understanding why cervical screening targets HPV DNA, not warts.

Australia has led the world in HPV disease prevention. The Gardasil 9 National Immunisation Program (NIP) has produced some of the steepest documented declines in both genital warts and high-grade cervical lesions of any country. Australia is on track to be the first country to eliminate cervical cancer as a public health problem, projected by 2035.

A. Core clinical — the AU general practice framework

Who is at risk and how HPV spreads

HPV spreads by skin-to-skin contact — predominantly sexual, but also through close contact with infected skin beyond areas covered by condoms. This is why condoms significantly reduce — but do not eliminate — HPV transmission. The virus is extremely common; a new sexual partner always carries some HPV transmission risk regardless of the partner’s apparent health.

Genital warts most commonly appear in sexually active people aged 15–30. The peak is in young adults, correlating with higher rates of new sexual partnerships. Post-vaccine, rates have fallen dramatically in cohorts vaccinated as adolescents.

In Australian surveillance data (Australian Government sexual health trends), genital wart notifications fell by over 90% in young women and by a striking amount in young men within years of Gardasil 4 introduction in 2007, reflecting both direct vaccine effect and population-level herd immunity.

Recognising genital warts

Genital warts are a clinical diagnosis — no laboratory test is needed in typical cases. They typically appear as:

Condylomata acuminata — soft, fleshy, cauliflower-like growths, pink to skin-coloured
Papular warts — smooth, dome-shaped papules, sometimes pigmented
Keratotic warts — thicker, harder surface, on hair-bearing skin or the penile shaft
Flat (sessile) warts — on the cervix or vagina, often subclinical

Sites in women: vulva (labia, introitus), perineum, perianal skin, vagina, cervix. Sites in men: penile shaft, glans, foreskin, scrotum, perianal skin (especially in men who have sex with men). Oral and pharyngeal warts occur occasionally.

When to biopsy: a wart that is pigmented, ulcerated, indurated, fixed, or atypical; any lesion that fails to respond to two appropriate treatment courses; any lesion in an immunocompromised patient; anyone over 40 with a new or changing vulvar lesion. These features can indicate VIN (vulvar intraepithelial neoplasia) or vulvar squamous cell carcinoma.

Differential diagnosis

A number of normal anatomical variants and conditions resemble warts:

Pearly penile papules (normal; arranged in a ring around the corona)
Vestibular papillae in women (normal; symmetrical, small projections at the vaginal entrance)
Fordyce spots (sebaceous glands on the labia or shaft — normal)
Molluscum contagiosum (dome-shaped, umbilicated; different virology)
Condyloma lata (secondary syphilis — flat, moist; confirm with RPR/syphilis serology)
Skin tags
Seborrhoeic keratoses (older patients; keratotic)

Syphilis must not be missed when any wart-like lesion is present — eTG recommends syphilis serology as part of the assessment when any uncertainty exists.

Full STI screen

ASHM guidelines recommend a full STI screen for all patients diagnosed with genital warts:

NAAT swab (vaginal, endocervical, or first-pass urine) for chlamydia and gonorrhoea
Syphilis serology (RPR/EIA)
HIV serology
Hepatitis B surface antigen if vaccination or immune status is uncertain
Confirm cervical screening is up to date (NCSP)

Treatment

The immune system clears the underlying HPV infection over time — typically within 6–18 months in most people — independent of topical treatment. Treatment removes visible warts and reduces symptoms. The choice of treatment depends on wart size, number, site, keratinisation, pregnancy status, immune status, patient preference, and access.

Observation: spontaneous regression occurs in approximately 30% of cases within 4 months. Small, asymptomatic warts in an otherwise well, non-pregnant person can be managed expectantly if preferred.

Patient-applied treatments (at home)

ASHM guidelines and eTG list two main options:

Podophyllotoxin 0.5% paint or 0.15% cream (Wartec) — PBS-listed for external genital and perianal warts. Applied twice daily for 3 days, then 4 days off; cycle repeated weekly for up to 4–6 weeks. For external warts only — not for internal (vaginal, cervical, anal canal, oral) use. Avoid in pregnancy (Category D — teratogenic). Local skin irritation is expected; reduce frequency if severe. Available at pharmacies.

Imiquimod 5% cream (Aldara) — PBS Authority Required (Streamlined) for external genital and perianal warts. Applied to the wart area three nights per week; left for 6–10 hours then washed off. Continue for up to 16 weeks. Imiquimod works by activating local innate immunity (Toll-like receptor 7 agonist) — it stimulates the skin’s immune response to clear the wart. This mechanism may explain the more durable response seen with imiquimod versus podophyllotoxin in some studies. Local erythema and erosion are expected side effects — reduce frequency if severe. In pregnancy: avoid in the first trimester (Category B1; limited data).

Clinician-applied treatments (in clinic)

Cryotherapy with liquid nitrogen: first-line in-clinic treatment. Liquid nitrogen is applied with a cotton-tip applicator or cryospray gun to produce a freeze-thaw cycle with a 1–2 mm halo of treated tissue around the wart. Repeat at 1–2 week intervals until clearance. Pain, blistering, and temporary hypopigmentation are common. Safe in pregnancy. Quick, inexpensive, and accessible in general practice.

Trichloroacetic acid (TCA) 80–90%: a caustic agent applied directly to the wart with a cotton-tipped applicator; surrounding skin protected with petroleum jelly. Effective and safe in pregnancy. Less commonly used than cryotherapy due to skill requirements and caustic nature.

Electrocautery and laser: for larger, more extensive, or refractory warts; require local or general anaesthesia. Smoke evacuation is essential during electrocautery and laser — HPV particles are present in the plume.

Surgical excision: for large pedunculated warts, or when histology is needed to exclude malignancy.

B. The HPV vaccine — Australia’s prevention success

The Gardasil 9 vaccine (9-valent HPV vaccine) covers types 6, 11, 16, 18, 31, 33, 45, 52, and 58 — preventing both genital warts (types 6 and 11) and the majority of HPV-driven cancers (types 16, 18, and five other high-risk types).

ATAGI recommends:

National Immunisation Program (NIP) — free schedule:

Age 12–13 (school-based, all genders) — 2-dose schedule, doses 6–12 months apart
Catch-up to age 25 — NIP-funded since 2018; opportunistic at every consultation for eligible young adults
Ideally administered before sexual debut but retains substantial benefit even after some sexual activity — it protects against types not yet acquired

3-dose schedule (0, 2, 6 months): required for anyone starting vaccination at age 15 or over, and for immunocompromised patients.

Adults aged 26–45: Gardasil 9 is TGA-approved and can be prescribed privately. Benefit diminishes the more types have already been acquired, but some benefit remains. Cost is approximately $200–250 per dose (3 doses needed). Individual decision based on sexual history and risk assessment.

Safety: large post-marketing surveillance studies across multiple countries confirm a strong safety profile. Local injection-site reactions (pain, redness, swelling) are very common; rare anaphylaxis (approximately 1.7 per million doses) requires the standard 15-minute post-injection observation. No causal link with chronic illness or autoimmune disease has been established in datasets involving tens of millions of doses.

C. Cervical screening — HPV-based testing and self-collection

The National Cervical Screening Program (NCSP) replaced Pap smears with HPV DNA testing in December 2017. This was a significant change in screening philosophy — from looking for abnormal cells to finding the virus that causes those cells to become abnormal.

Current NCSP schedule:

Ages 25–74, every 5 years if HPV-negative
HPV 16/18 detected → direct referral to colposcopy
Other high-risk HPV detected → reflex LBC (liquid-based cytology); manage per result
HPV-negative → 5-year routine recall
Exit screening at age 70–74 if last two screens were negative

Self-collection has been available since July 2022 and is fully equivalent to clinician-collected samples for HPV detection. Women who prefer to collect their own vaginal swab — for any reason, including discomfort, previous trauma, or access barriers — achieve the same screening accuracy. Ask your GP for the self-collection option at your next cervical screen appointment.

Note: a positive cervical screening result for high-risk HPV does not mean cancer. It means follow-up investigation is needed to determine whether precancerous changes are present. Most HPV infections clear without causing any lasting change.

Genital warts do not require additional cervical screening — the wart-causing types (6 and 11) are not associated with cervical cancer, and a wart diagnosis does not change the NCSP recall interval.

D. Anal cancer screening for high-risk groups

Anal cancer is strongly linked to high-risk HPV (predominantly type 16). In the general population, anal cancer is rare. In people living with HIV who have sex with men, rates are 70–100 times higher than background.

The ANCHOR trial (2022) demonstrated that treating high-grade anal squamous intraepithelial lesions (HSIL) reduces anal cancer incidence by approximately 57% — establishing the value of anal cancer surveillance in high-risk groups.

Cancer Council Australia and the Australian Anal Cancer Working Group recommend:

Annual digital anorectal examination (DARE) for HIV-positive men who have sex with men aged 35 and over
Anal cytology and high-resolution anoscopy (HRA) in centres with expertise for higher-risk individuals

Referral to a sexual health clinic or specialist proctology service is appropriate for this population.

E. Australian operations — MBS, PBS, and referrals

Standard GP consultation items (23, 36, 44) apply. For cryotherapy procedures, confirm the relevant skin lesion treatment MBS item number at MBS Online for the specific site and clinical context.

PBS listing: imiquimod 5% (Aldara) — Authority Required (Streamlined) for external genital and perianal warts; podophyllotoxin 0.5% paint (Wartec) — general PBS listing. The HPV vaccine is NIP-funded for eligible ages; private prescription for adults 26–45.

Referral pathways:

Sexual health clinic — complex or refractory warts; immunocompromised patients; high-risk MSM requiring anal surveillance; pregnancy-complicated warts
Gynaecology/colposcopy — abnormal NCSP result; cervical or vaginal warts
ENT — oral or pharyngeal lesions
Colorectal/proctology or sexual health — anal canal warts; suspected anal HSIL; HRA referral

E. Special populations

Pregnancy: avoid podophyllotoxin (Category D). Imiquimod: avoid in the first trimester. Cryotherapy or TCA are the preferred options in pregnancy. Warts often proliferate during pregnancy due to immune changes, and frequently regress postpartum without treatment. The risk of laryngeal papillomatosis in the neonate from vaginal HPV exposure is very low (less than 1 in 1,000 vaginal deliveries) and is not a routine indication for caesarean section.

Immunocompromised patients (HIV, transplant, immunosuppressive therapy): warts are more extensive, more refractory, and associated with a higher risk of progression to intraepithelial neoplasia or invasive cancer. Biopsy threshold is lower; specialist co-management is recommended.

Children with anogenital warts: warts under age 4 are usually vertically transmitted (from mother at delivery or during early childhood) and are managed conservatively. Any warts in a child aged over 4 require assessment for possible sexual abuse by an experienced paediatric or forensic specialist.

Aboriginal and Torres Strait Islander communities: opportunistic HPV vaccination and cervical screening at every health encounter is supported by RACGP Red Book recommendations. The item 715 health assessment is an important opportunity.

When to escalate

Seek medical review or refer if:

Any wart is pigmented, ulcerated, indurated, or does not respond to two treatment courses — biopsy needed
Warts involve the anal canal or inside the vagina — specialist assessment
Warts in pregnancy — management per site above
Immunocompromised patient — sexual health or specialist input
Abnormal cervical screening result — follow the NCSP pathway to colposcopy
Significant distress or anxiety post-diagnosis — counselling support is appropriate

What this article is and is not

This is general health information drawn from ASHM Australian STI Management Guidelines, eTG, ATAGI, Cancer Council Australia, and AMH. It does not constitute personal medical advice. Discuss your own situation with your GP, who can assess and manage your specific circumstances.

Australian consumer resources: HealthDirect — Genital warts, Better Health Channel — Genital warts.

For crisis support: Lifeline 13 11 14, Beyond Blue 1300 22 4636.

Sources cited

Frequently asked questions

What is the difference between the HPV types that cause warts and those that cause cancer?

HPV has over 200 genotypes. The types that cause genital warts — predominantly HPV 6 and 11 — are called low-risk types because they almost never cause cancer. The types associated with cancer — especially HPV 16 and 18, plus types 31, 33, 45, 52, and 58 — are called high-risk types. They can cause cancer of the cervix, anus, vulva, vagina, penis, and throat without producing any visible warts. This is why cervical screening (looking for high-risk HPV DNA) and HPV vaccination are the key cancer-prevention tools, while treatment of visible warts is a separate issue. The [Gardasil 9 vaccine](https://immunisationhandbook.health.gov.au) protects against both the wart-causing types (6 and 11) and the most important cancer-causing types (16, 18, 31, 33, 45, 52, 58) in a single vaccine.
What treatments are available for genital warts in Australia?

Treatment options fall into patient-applied and clinician-applied categories. Patient-applied: **podophyllotoxin 0.5% paint or 0.15% cream (Wartec)** — applied to external warts twice daily for 3 days, then 4 days off, repeated weekly for up to 6 weeks; not used in pregnancy. **Imiquimod 5% cream (Aldara)** — applied to external warts three nights per week, washed off after 6–10 hours, for up to 16 weeks; it works by activating the immune system at the site. Clinician-applied: **cryotherapy with liquid nitrogen** is the most accessible in-clinic option — the wart is frozen with a brief freeze-thaw cycle, repeated every 1–2 weeks until clearance. Trichloroacetic acid (TCA) is an alternative used in clinic and is safe in pregnancy. Larger or refractory warts may need electrocautery, laser, or surgical excision by a specialist. No treatment cures the underlying HPV infection — the immune system clears the virus over time. Recurrence within 3 months is common even after complete clearance.
I've been vaccinated. Can I still get genital warts?

Yes, though much less commonly. Gardasil 9 provides strong protection against HPV types 6 and 11 (which cause ~90% of warts) when given before any exposure to those types — usually before sexual activity starts. If vaccination occurred after some sexual activity, or after a previous HPV infection with those types, the vaccine protects against types not yet acquired but cannot clear types already present. Australia's post-vaccine data show more than a 90% reduction in genital warts diagnoses among vaccinated cohorts, with a significant herd-protection effect in unvaccinated individuals too. Some warts in vaccinated people are caused by types not covered by the vaccine.
What is the cervical screening self-collection option?

Since July 2022, self-collected vaginal swabs have been a fully equivalent option within the National Cervical Screening Program (NCSP). You take your own vaginal swab — in private, in the GP's room — and it is sent for the same HPV-based test as a clinician-collected sample. Detection rates for high-risk HPV DNA are equivalent between the two methods. Self-collection is particularly valuable for women who have delayed screening due to discomfort, trauma, or difficulty accessing a clinician. Ask your GP for the self-collection kit if you would prefer this option — it does not reduce the quality of your screening result.
Does having a wart diagnosis mean I have to tell my partner?

Genital warts are not formally notifiable to health authorities in Australia, so there is no legal obligation to report. However, sexual partners should be made aware that they may have been exposed to HPV — principally so they can ensure their own cervical screening is up to date and consider HPV vaccination if they are eligible. Treating warts in your partner does not prevent you being re-exposed, because they have likely already been exposed to the same virus. Condoms reduce but do not eliminate HPV transmission — HPV spreads by skin-to-skin contact over a wider area than condoms cover. A wart diagnosis does not necessarily indicate recent infidelity, as HPV can remain dormant for months to years before warts become visible.

Source quality

Sources grouped by evidence tier. AU primary tier first; international where AU is silent or lagging; named-author reconstruction where guidelines have not yet caught up. How tiers work.