Anal squamous cell carcinoma is a rare cancer that develops in the tissues lining the anal canal or near the anal opening. Although uncommon, affecting approximately 11,000 people annually in the United States, this disease is highly treatable when detected early, especially since it’s closely linked to a preventable virus infection.

How Common Is Anal Squamous Cell Carcinoma?

Anal squamous cell carcinoma represents a small portion of all cancers affecting the digestive system. It accounts for roughly 4 percent of all tumors in the anorectal region, making it an uncommon diagnosis compared to other gastrointestinal cancers.^[2] Despite its rarity, the number of cases has been steadily climbing during the second half of the 20th century and continuing into the 21st century, with incidence rates increasing by more than 2.9 percent compared to earlier decades.^[6]

Only about 11,000 individuals receive this diagnosis each year in the United States, with an estimated 2,030 deaths annually.^[1][10] The rising incidence appears closely tied to the increased prevalence of human papillomavirus infection in the population. The good news is that survival rates have improved significantly over the past several decades, particularly for patients diagnosed with early-stage disease.^[6]

Most anal cancers are squamous cell carcinomas, meaning they develop in the flat cells that line the anal canal and the skin around the anal opening. This type makes up more than 80 percent of all anal cancers.^[4] At the time of diagnosis, most people have relatively small tumors measuring 5 centimeters or less, and fewer than 20 percent have cancer that has spread to nearby lymph nodes. For these early-stage patients, five-year survival rates exceed 85 percent.^[10]

What Causes Anal Squamous Cell Carcinoma?

The primary cause of anal squamous cell carcinoma is infection with certain high-risk strains of human papillomavirus, commonly called HPV. This is the same virus responsible for cervical cancer in women. HPV is a sexually transmitted infection that is extremely common, and most people who contract it never experience any symptoms or know they have it.^[1]

Among anal cancer cases, approximately 95 percent are related to HPV infection, with the highest risk associated with serotypes 16 and 18.^[10] In research studies from Scandinavia, HPV DNA from serotype 16 was detected in 73 percent of anal cancer tissue samples, and either serotype 16, 18, or both were found in 84 percent of specimens. Interestingly, no rectal cancer samples contained HPV DNA, highlighting the specific connection between HPV and anal cancer.^[3]

The virus causes changes in the cells lining the anal canal through a complex inflammatory process. When HPV DNA integrates into the cells’ genetic material, it appears to be the driving mechanism that leads to cancer development.^[2] Anal squamous cell carcinoma typically develops at the point where different types of cells meet in the anal canal, arising from a precancerous condition called high-grade anal intraepithelial neoplasia.^[3]

However, it’s crucial to understand that most people infected with HPV never develop anal cancer. The infection is very widespread, affecting about 10 percent of women worldwide at any given time, yet anal cancer remains rare.^[3] Additionally, not everyone diagnosed with anal cancer has HPV, though the vast majority do.^[1]

Who Is at Higher Risk?

Beyond HPV infection itself, several factors increase a person’s chances of developing anal squamous cell carcinoma. Understanding these risk factors can help identify individuals who might benefit from closer monitoring or preventive measures.

Sexual practices play a significant role in risk. Engaging in receptive anal intercourse, regardless of biological sex, increases exposure to HPV in the anal area. This risk applies to everyone who participates in this activity, and having multiple sexual partners over a lifetime further elevates the risk because it increases the likelihood of HPV exposure.^[1][10] A history of other sexually transmitted diseases also contributes to higher risk.^[6]

Having HIV (human immunodeficiency virus) substantially increases anal cancer risk. HIV weakens the immune system, making it less effective at fighting off other viruses like HPV. Many people with anal cancer have both HPV and HIV infections simultaneously.^[1] More broadly, any condition or medication that weakens the immune system raises risk, including immunosuppression following organ transplantation, blood disorders, or immunological conditions.^[1][6]

People who have had other cancers affecting the genital area face increased risk as well. This is particularly true for individuals with a history of vulvar, vaginal, or cervical cancer, all of which share the common link to HPV infection.^[1][6]

Smoking is another major risk factor. People who smoke are more likely to develop anal cancer, as well as many other types of cancer. The harmful chemicals in tobacco smoke can damage cells throughout the body, including those in the anal area.^[1][6]

Not being vaccinated against HPV increases risk because the vaccine protects against the specific viral strains most likely to cause cancer. The HPV vaccine not only helps prevent anal cancer but also protects against cancers of the mouth, throat, cervix, and penis.^[1]

Recognizing the Symptoms

Anal squamous cell carcinoma often produces symptoms that can easily be confused with common, non-cancerous conditions like hemorrhoids. This similarity sometimes leads to delays in diagnosis, as people may wait to seek medical attention thinking they have a minor problem that will resolve on its own.^[3]

The most common symptom is rectal bleeding or noticing blood in the stool. This occurs in about 45 percent of patients and is often the first sign that prompts someone to visit a healthcare provider.^[6][1] While rectal bleeding can result from many benign causes, it should always be evaluated by a medical professional, especially if it persists for more than a few days or worsens over time.

Many people experience pain or a sensation of fullness in the anal area. This might feel like constantly needing to have a bowel movement, even after using the bathroom. Some describe it as pressure or discomfort that doesn’t go away.^[1][6]

Changes in bowel habits are another important warning sign. Stools may become thinner than usual, or patterns of bowel movements may change in frequency. These alterations occur because a growing tumor can partially block the anal canal, affecting how waste moves through and exits the body.^[1]

A visible or palpable lump or mass at the anal opening can sometimes be felt or noticed during bathing or cleaning. Additionally, persistent itching around the anus may occur, though this is also a very common symptom of many benign conditions.^[1]

It’s important to emphasize that having one or more of these symptoms doesn’t necessarily mean you have anal cancer. Hemorrhoids, anal fissures, and other common conditions cause identical symptoms far more often than cancer does. However, any persistent or worsening symptoms warrant medical evaluation to rule out serious conditions.^[1]

One challenge with anal cancer is that it doesn’t always cause symptoms in the early stages. This is why screening tests may be particularly valuable for people at high risk, even when they feel completely fine.^[1]

How to Lower Your Risk

While there’s no guaranteed way to prevent anal squamous cell carcinoma, several concrete steps can significantly reduce your chances of developing this disease. Prevention focuses primarily on avoiding HPV infection and strengthening your body’s ability to fight off potential cancer-causing changes.

Getting the HPV vaccine is one of the most effective prevention strategies, especially when received before exposure to the virus. The vaccine protects against the specific HPV strains most commonly linked to cancer. It’s most effective when given to young people before they become sexually active, but adults may also benefit. Beyond anal cancer, this vaccine prevents multiple other cancers including those affecting the cervix, penis, mouth, and throat.^[1][3]

Using condoms during anal sex reduces the risk of HPV transmission, though they don’t provide complete protection since HPV can affect areas not covered by a condom. Still, consistent condom use offers significant protection against HPV and other sexually transmitted infections.^[1]

If you smoke, quitting is crucial. Smoking increases the risk of anal cancer and virtually all other cancer types. If you don’t smoke, don’t start. The chemicals in tobacco damage cells throughout your body and impair your immune system’s ability to eliminate abnormal cells before they become cancerous.^[1]

For people with significant risk factors, discussing screening options with a healthcare provider may be worthwhile. Unlike some other cancers, routine screening for anal cancer isn’t standard for the general population. However, certain high-risk individuals might benefit from screening tests such as an anal Pap test (similar to cervical Pap tests) or an anal HPV test. These tests examine tissue samples for abnormal cells or the presence of HPV virus.^[1]

Who might benefit from screening? People with HIV infection, those who have had organ transplants, individuals with a history of genital cancers, and others with weakened immune systems should ask their healthcare providers whether screening makes sense for them. The presence of precancerous changes called anal intraepithelial neoplasia in high-risk groups indicates the need for ongoing surveillance through specialized examination techniques.^[3]

Changes That Occur in the Body

Understanding what happens inside the body when anal squamous cell carcinoma develops helps explain both the symptoms and the treatment approaches. The disease process begins at the cellular level and involves complex interactions between viruses and the body’s normal defense systems.

The anal canal has a unique structure where different types of cells meet, creating a junction called the squamocolumnar epithelium. This is the area where the moist, mucus-producing cells of the inner digestive tract transition to the protective squamous cells that line the outer portion of the canal and the skin around the anus. This junction point is particularly vulnerable to HPV-related changes.^[3]

When high-risk HPV strains infect cells in this region, the viral DNA can integrate into the host cell’s genetic material. This integration appears to be the key mechanism that drives cancer development. The inserted viral genes disrupt the cell’s normal growth controls, causing cells to multiply abnormally and accumulate mutations over time.^[2]

Before cancer fully develops, infected cells go through precancerous stages. These stages are collectively called anal intraepithelial neoplasia, classified as low-grade or high-grade depending on how abnormal the cells appear under a microscope. High-grade anal intraepithelial neoplasia represents cells that are very abnormal and have a higher likelihood of progressing to invasive cancer if left untreated.^[3]

HPV infection triggers inflammation in the affected tissues. This chronic inflammatory process creates an environment where normal cellular controls break down, increasing the likelihood that dysplasia (abnormal cell growth) will progress to cancer. The same inflammatory pathway is seen in cervical cancer, which shares HPV as its primary cause.^[3]

As cancer cells accumulate and form a tumor, they can grow in size and potentially spread beyond their original location. The anal canal has lymphatic drainage that follows the inguinal vessels, meaning cancer cells can travel to lymph nodes in the groin area. Tumor size and whether cancer has reached the lymph nodes are the two most important factors affecting prognosis.^[10]

When a tumor grows within the anal canal, it can physically obstruct the passage, explaining why stools become thinner and bowel movements may change. Tumors may also bleed easily, especially during bowel movements, which accounts for the blood in stools many patients notice. As the tumor enlarges, it can cause pain and the sensation of pressure or fullness that patients commonly report.^[1]

In advanced cases, if not detected and treated early, cancer cells may spread to distant organs through the bloodstream. However, most anal cancers are diagnosed before this occurs. The two-year survival rate for patients with primary tumors smaller than 2 centimeters is significantly better than for those with larger tumors, underscoring the importance of early detection.^[10]

The body’s immune system plays a critical role in fighting cancer development. A healthy immune system can often recognize and destroy abnormal cells before they form tumors. This explains why people with weakened immune systems, whether from HIV, immunosuppressive medications, or other conditions, face substantially higher risk. Their immune systems are less capable of eliminating HPV-infected cells or destroying precancerous cells before they progress to cancer.^[1]