Anal dysplasia is the abnormal growth of cells lining the anal canal, considered a precancerous condition that can, in some cases, progress to anal cancer. It is almost always caused by human papillomavirus (HPV) infection and is graded on a spectrum from low-grade changes that often resolve on their own to high-grade changes that carry a meaningful risk of becoming cancerous if left untreated.
How Anal Dysplasia Is Classified
Doctors categorize anal dysplasia into two tiers using terminology standardized by the Lower Anogenital Squamous Terminology (LAST) project. The simpler, earlier form is called low-grade squamous intraepithelial lesion (LSIL), which corresponds to what was previously labeled AIN-1. In LSIL, abnormal cells appear only on the surface layer of the anal lining, and the overall tissue structure stays mostly intact.
The more concerning form is high-grade squamous intraepithelial lesion (HSIL), which covers what used to be called AIN-2 and AIN-3. In HSIL, abnormal cells extend deeper into the tissue, the cells lose their normal maturation pattern, and their internal structures look increasingly disorganized under a microscope. HSIL is the stage that warrants treatment because of its potential to progress to invasive squamous cell carcinoma.
The Role of HPV
HPV is the driving force behind nearly all anal dysplasia. The virus infects the thin, flat cells lining the anal canal and, over time, can cause them to grow abnormally. Not all HPV strains carry the same risk. HPV 16 and HPV 18 are classified as high-risk types because of their strong link to cancer development. Together they account for the majority of anal dysplasia and anal cancer cases, though roughly 8% of anal cancers are caused by other high-risk HPV strains.
Most people who contract HPV clear the virus naturally within one to two years. Dysplasia develops when the infection persists, giving the virus time to alter cell growth at a deeper level.
Who Is Most at Risk
Certain groups face a significantly higher chance of developing anal dysplasia. People living with HIV are at the top of that list. In one study of 317 HIV-positive individuals, 48% had abnormal anal cell results on screening. Among those who went on to have biopsies, 62% were found to have high-grade lesions. Broader research has found rates of abnormal anal cytology ranging from 27% in women with HIV to as high as 94% in urban populations of HIV-positive men who have sex with men.
Beyond HIV, other risk factors include:
- Men who have sex with men (MSM), regardless of HIV status
- Immunosuppression from organ transplant medications or other causes
- History of other HPV-related cancers or precancers, such as cervical or vulvar dysplasia
- Smoking, which impairs the body’s ability to clear HPV
- Receptive anal intercourse, which increases exposure to HPV in the anal canal
Symptoms and Warning Signs
The most important thing to know about anal dysplasia is that it usually produces no symptoms at all. In one study published in JAMA Surgery, 69% of patients with confirmed dysplasia were completely asymptomatic. When symptoms do occur, they tend to be nonspecific: bleeding was reported in 15% of patients, anal pain in 12%, and itching in 11%. People with dysplasia (either grade) were more than four times as likely to have visible anal lesions on physical exam compared to those without dysplasia, but many of those lesions went unnoticed by the patients themselves.
Because symptoms are unreliable, screening is the primary way anal dysplasia gets caught.
How It Is Diagnosed
Screening typically starts with an anal Pap test, which works much like a cervical Pap smear. A clinician inserts a small swab into the anal canal, collects a sample of cells, and sends it to a lab for examination. The sensitivity of anal cytology ranges from 69% to 93%, meaning it catches most abnormalities but can miss some. Its specificity is lower, between 32% and 59%, so a positive result doesn’t always mean dysplasia is present.
If the Pap test comes back abnormal, the next step is high-resolution anoscopy (HRA). During this procedure, a clinician uses a small scope with a magnifying lens to examine the anal canal closely. A dilute acetic acid solution (essentially vinegar) is applied to the tissue, which causes abnormal areas to turn white and become visible. Suspicious spots are biopsied and sent for analysis, which gives the definitive diagnosis and grade.
Risk of Progressing to Cancer
Low-grade dysplasia frequently resolves without treatment as the immune system clears the underlying HPV infection. High-grade dysplasia is a different story. In a large nationwide study tracking 1,222 people with AIN-3 (the most advanced precancerous grade), 97 individuals, or 7.9%, went on to develop invasive anal squamous cell carcinoma over approximately 10 years of follow-up. That progression rate is high enough that treatment of HSIL is now considered standard practice, especially after the landmark ANCHOR trial demonstrated that treating high-grade lesions in people with HIV cut their anal cancer risk by more than half.
Treatment Options
Treatment for anal dysplasia focuses on destroying or removing the abnormal tissue before it has a chance to become cancerous. The approach depends on the size, number, and location of the lesions.
Office-Based Ablation
The two most common in-office procedures are infrared coagulation (IRC) and electrocautery (also called hyfrecation). Both use targeted energy to burn away abnormal tissue. In a randomized trial comparing IRC to active monitoring, 62% of patients treated with IRC had complete clearance of their target lesion at 12 months, compared to just 30% in the monitoring group. The overall disease-free rate at 12 months was 71% for treated patients versus 28% for those who were monitored only.
Recurrence is common with ablation. About 47% of treated patients developed new high-grade lesions at different sites within 12 months, and roughly 15% of those who initially achieved clearance saw their original lesion return during the second year. Electrocautery showed a similar recurrence rate of 43% at 48 weeks in one prospective trial. This means ongoing surveillance after treatment is essential.
Topical Treatments
For some patients, topical creams applied directly to the anal canal can treat dysplasia. One option involves applying an immune-boosting cream once daily for 16 weeks, which works by stimulating the body’s own antiviral response against HPV-infected cells. Another uses a chemotherapy cream applied twice daily for five days at a time, repeated every two weeks for eight cycles. Both approaches are studied primarily for perianal and intra-anal high-grade lesions. They can cause local irritation and discomfort, and are generally reserved for cases where ablation isn’t ideal or as a complement to other treatments.
Surgical Excision
For larger or more extensive lesions, surgical removal under anesthesia may be necessary. This is also the preferred approach when there’s concern that a lesion may already contain early invasive cancer, since excision provides a complete tissue sample that pathologists can examine for deeper invasion.
Prevention Through Vaccination
The HPV vaccine is highly effective at preventing the infections that cause anal dysplasia. A systematic review pooling data from six clinical trials and eight real-world studies found that vaccination at age 26 or younger reduced anal HPV infections by 77% to 84% in those who received the vaccine before being exposed to the virus. The vaccine also showed significant effectiveness in preventing anal intraepithelial neoplasia in this age group.
The picture is less clear for people vaccinated after age 26, particularly those living with HIV. Studies in that population did not find a statistically significant protective effect against anal HPV infection or dysplasia, likely because most participants had already been exposed to HPV. This reinforces the value of vaccination earlier in life, ideally before sexual activity begins. The CDC currently recommends routine HPV vaccination starting at ages 11 to 12, with catch-up vaccination available through age 26.
Ongoing Monitoring Matters
Because anal dysplasia recurs frequently even after successful treatment, follow-up is a long-term commitment. Most specialists recommend repeat high-resolution anoscopy every 6 to 12 months after treatment for high-grade disease. For people in high-risk groups who haven’t yet been diagnosed, regular screening with anal cytology can catch dysplasia before it progresses. The ANCHOR trial provided the first strong evidence that this screen-and-treat approach meaningfully reduces anal cancer risk in people with HIV, and it is likely to shape screening recommendations for other at-risk populations in the coming years.