Anal Intraepithelial Neoplasia (AIN): Understanding Your Pathology Report

by Jason Wasserman MD PhD FRCPC
December 21, 2025

Anal intraepithelial neoplasia (AIN) is a precancerous condition that affects the cells lining the anus and anal canal. In this condition, the surface cells show abnormal changes, but they have not spread into deeper tissues, which means it is not cancer. However, some cases can progress over time to squamous cell carcinoma of the anus.

The risk of progression depends mainly on the grade of the disease, which reflects how abnormal the cells look under the microscope and how much of the lining is involved. Anal intraepithelial neoplasia may also be described as a squamous intraepithelial lesion, a term used to refer to abnormal squamous cells limited to the surface lining.

Where does anal intraepithelial neoplasia start?

Anal intraepithelial neoplasia starts in the epithelium, the thin layer of cells that lines the anal canal. The anal canal is the short passage at the end of the digestive tract that connects the rectum to the outside of the body. The lining cells in this area are called squamous cells, similar to the cells found on the skin. When these squamous cells develop abnormal changes but remain confined to the epithelium, the diagnosis is anal intraepithelial neoplasia.

What are the symptoms of anal intraepithelial neoplasia?

Many people with anal intraepithelial neoplasia have no symptoms, and the condition is often found during routine screening or examination for another reason.

When symptoms are present, they may include:

• Bleeding from the anus.

• Itching or irritation around the anus.

• Discomfort or a small lump near the anal opening.

These symptoms are common and can be caused by many noncancerous conditions, which is why a biopsy is often needed to make the diagnosis.

What causes anal intraepithelial neoplasia?

Most cases are caused by long-standing infection with human papillomavirus (HPV), a widespread virus spread through skin-to-skin contact.

• Low-grade anal intraepithelial neoplasia is usually associated with low-risk HPV types, such as HPV 6 and 11.

• High-grade anal intraepithelial neoplasia is most often associated with high-risk HPV types, especially HPV 16, but also HPV 18, 31, 33, and others.

High-risk HPV interferes with normal cell growth and repair, allowing abnormal cells to persist and accumulate over time.

Is anal intraepithelial neoplasia a type of cancer?

No. Anal intraepithelial neoplasia is not cancer. The abnormal cells are confined to the surface lining and have not invaded deeper tissues.

However, because these abnormal cells can develop into squamous cell carcinoma if left untreated, anal intraepithelial neoplasia is considered a precancerous condition.

What is the risk of developing cancer?

The risk depends primarily on the grade of anal intraepithelial neoplasia and individual risk factors.

• Low-grade disease has a very low risk of progression and often resolves on its own.

• High-grade disease has a higher risk, especially when abnormalities involve most or all of the epithelial thickness.

Studies suggest that if left untreated, approximately 10–15% of people with the highest-grade disease may develop anal cancer over several years.

Risk is increased by:

• Persistent infection with high-risk HPV (especially HPV 16).

• A weakened immune system, such as HIV infection or organ transplantation.

• Smoking.

• Chronic inflammation or irritation of the anal area.

How is this diagnosis made?

The diagnosis is made by a pathologist examining a tissue sample under the microscope. The tissue is usually obtained through a biopsy, where a small piece of the anal lining is removed.

Under the microscope, the pathologist looks for:

• Abnormal cell size and shape.

• Darkened or irregular nuclei.

• Abnormal patterns of cell division.

• How much of the epithelial thickness is involved.

Immunohistochemistry for p16

Cells infected with high-risk HPV often produce large amounts of a protein called p16. Pathologists use a special test called immunohistochemistry to detect this protein.

• Strong, diffuse p16 staining supports a diagnosis of high-grade anal intraepithelial neoplasia.

• p16 helps distinguish true high-grade disease from benign or reactive changes that can look similar under the microscope.

HPV in situ hybridization (HPV ISH)

Another test that may be performed is HPV in situ hybridization (HPV ISH). This test directly looks for HPV genetic material in the tissue.

• HPV ISH can identify whether HPV is present and, in some cases, whether it is a high-risk type.

• This test is especially useful when the diagnosis is uncertain or when additional confirmation of HPV involvement is needed.

How is anal intraepithelial neoplasia graded?

Pathologists divide anal intraepithelial neoplasia into three grades based on how abnormal the cells appear under the microscope and how much of the epithelial lining is affected.

Grading is important because it helps estimate the risk of progression to cancer and guides decisions about monitoring and treatment. Lower grades usually require observation, while higher grades often need closer follow-up or treatment.

Anal intraepithelial neoplasia 1

In anal intraepithelial neoplasia 1, abnormal cells are confined to the lower one-third of the epithelium. Cells infected with HPV, called koilocytes, are commonly seen. This is considered a low-grade disease and has a very low risk of progressing to cancer. When the lesion forms a visible growth, it may be called a condyloma acuminatum.

Anal intraepithelial neoplasia 2

In anal intraepithelial neoplasia 2, abnormal cells involve the lower two-thirds of the epithelium. The cells appear larger and darker, and more dividing cells are usually present. This is considered high-grade disease and carries a higher risk of progression than low-grade disease.

Anal intraepithelial neoplasia 3

In anal intraepithelial neoplasia 3, abnormal cells extend almost to the full thickness of the epithelium. The cells show marked abnormalities, and many dividing cells are typically seen. This represents the highest grade and carries the greatest risk of progression to anal squamous cell carcinoma if left untreated.

Questions to ask your doctor

• What grade of anal intraepithelial neoplasia do I have?
• What is my risk of developing anal cancer?
• Do I need treatment or close monitoring?
• How often should I have follow-up exams or biopsies?
• Would HPV vaccination still be helpful for me?