Anal cancer is diagnosed through a combination of physical examination, visual inspection with specialized instruments, and tissue biopsy. The process typically starts with a doctor feeling for abnormalities during a digital rectal exam and, if something seems off, progresses to high-resolution anoscopy and a biopsy to confirm whether cancer cells are present.
Why Anal Cancer Is Often Caught Late
One of the biggest challenges with anal cancer is that its early symptoms look a lot like hemorrhoids. Bleeding, pain, and changes in bowel habits overlap between the two conditions, and studies have found that primary care doctors misdiagnose anal cancer as hemorrhoids during about 27% of first visits. There are some differences worth knowing: hemorrhoid bleeding is typically bright red, while anal cancer bleeding can be dark or bright red. Hemorrhoid symptoms tend to come and go and improve with over-the-counter treatments, while anal cancer symptoms persist or worsen over time. Pain that steadily gets worse is more characteristic of cancer than hemorrhoids.
These overlapping symptoms are exactly why a thorough rectal examination matters when bleeding or pain doesn’t resolve with basic treatment.
The Digital Rectal Exam
The first diagnostic step is usually a digital rectal exam, where a doctor inserts a gloved, lubricated finger into the anal canal to feel for lumps, hardened areas, or other abnormalities. This is a quick exam that can be done in a regular office visit and doesn’t require any preparation. While it can’t confirm cancer on its own, it can detect masses or irregular tissue that warrant further investigation. Current HIV clinical guidelines recommend that men who have sex with men and transgender women with HIV undergo this exam annually starting at age 35, and all other people with HIV starting at age 45.
Anal Cytology (the Anal Pap Smear)
An anal Pap smear works much like a cervical Pap smear. A small brush or swab collects cells from the lining of the anal canal, and those cells are examined under a microscope for precancerous or cancerous changes. Results are reported using the same classification system as cervical Pap smears, ranging from normal (no abnormal cells) through categories like atypical cells of uncertain significance, low-grade abnormalities, and high-grade abnormalities.
Anal cytology is less accurate than its cervical counterpart. A meta-analysis comparing the two found that cervical screening had a diagnostic accuracy score of about 0.83, while anal screening scored around 0.70. That means anal Pap smears miss more abnormalities and produce more false results than cervical ones. For this reason, an abnormal anal Pap smear always leads to further testing rather than serving as a standalone diagnosis. Screening can also include testing for high-risk strains of HPV alongside the cytology.
High-Resolution Anoscopy
If a digital exam or Pap smear raises concerns, the next step is usually high-resolution anoscopy. This procedure combines a small, clear tube called an anoscope (which holds the anal canal open) with a colposcope, a high-powered microscope connected to a monitor. The magnified view lets the doctor examine the anal lining in detail.
During the procedure, the doctor typically soaks a cotton swab or gauze in a mild acetic acid solution (essentially diluted vinegar) and places it inside the anal canal for a few minutes. The acid reacts with abnormal cells and turns them white, making suspicious areas stand out against the normal pink tissue. This is the same technique used during cervical colposcopy. The procedure is done in an office or clinic setting and doesn’t require general anesthesia, though you may feel pressure or mild discomfort.
Biopsy: The Definitive Test
A biopsy is the only way to confirm anal cancer. During high-resolution anoscopy, the doctor removes small samples of any tissue that looks abnormal. These samples go to a pathology lab, where they’re examined under a microscope to determine whether cancer cells are present and, if so, what type.
Most anal cancers are squamous cell carcinomas, which arise from the flat cells lining the anal canal. Pathologists use specific protein markers to identify the tumor type when the cells look unusual or poorly differentiated. Squamous cell cancers of the anus test positive for certain proteins (CK5/6, p63) and negative for others (CK20), which helps distinguish them from rarer types like anal gland cancers, which show the opposite pattern.
HPV and p16 Testing After Diagnosis
Once anal cancer is confirmed, the biopsy tissue is often tested for high-risk HPV and a protein called p16, which becomes overproduced when HPV is actively driving cell growth. About 76% of anal squamous cell cancers test positive for both markers. This testing isn’t just academic. It carries real prognostic weight.
An individual patient data meta-analysis found that patients whose tumors were positive for both p16 and high-risk HPV DNA had a three-year survival rate of 86%. Patients whose tumors were negative for both, meaning the cancer was not HPV-related, had a three-year survival rate of just 39%. Patients with mixed results fell somewhere in between, with three-year survival rates of 55% to 75% depending on which marker was positive. These results help doctors and patients understand the likely course of the disease and can influence treatment planning.
Screening Schedules for High-Risk Groups
Certain groups face a significantly higher risk of anal cancer and benefit from regular screening before any symptoms appear. Federal HIV clinical guidelines recommend the following:
- Men who have sex with men and transgender women with HIV: Begin screening at age 35 with annual digital rectal exams and anal cytology, with or without HPV co-testing.
- All other people with HIV: Begin screening at age 45 with the same annual approach.
Additional risk factors that may prompt earlier or more urgent screening include a history of smoking, longer duration of immune suppression, a history of AIDS, and testing positive for HPV strains 16 or 18. People with any of these factors are generally referred for high-resolution anoscopy as soon as feasible, even without an abnormal Pap smear.
What the Diagnostic Process Feels Like
The digital rectal exam takes under a minute and involves brief discomfort. An anal Pap smear is similarly quick and feels like mild pressure. High-resolution anoscopy takes longer, usually 15 to 30 minutes, and can feel uncomfortable when the acetic acid is applied or when biopsy samples are taken, though the pain is typically manageable without sedation. Some mild bleeding or soreness after a biopsy is normal and usually resolves within a few days. Results from a biopsy typically come back within one to two weeks.
If cancer is confirmed, the next steps involve imaging (CT scans, MRI, or PET scans) to determine how far the cancer has spread, which guides the treatment approach.