There are multiple manifestations of anal HPV infection. 

• Anal HPV infection is very common but usually remains silent without any symptoms or signs. It can be diagnosed only with biopsy or PCR. No treatment is necessary. 
• Anal warts (condylomas) are the most common manifestation of anal HPV-infection. They are usually caused by low-risk HPV subtypes. Warts are small flat or like a cauliflower, the head of a pin or a pea. They may look as knuckles or be horny with pointed edges. They can get a large size if neglected. They are found usually in the anal canal and perianal skin. Usually, they do not cause pain or discomfort and patients remains unaware of the condition. Sometimes HPV infection causes extensive and flat velvety lesions with rough surface. They may cause stinging, severe itching and fluid discharge.
• Dysplasia. Precancerous dysplasias do not cause any discomfort and cannot be detected by simple visual examination. They can be diagnosed only with anal cytology or High Resolution Anoscopy.
• Anal cancer. Anal cancer is an uncommon malignancy that is associated closely with HPV infection. It is more frequent in high risk groups. In the very early stages there are no obvious symptoms.  Anal cancer is seen with bleeding, pain or fullness, abnormalities in bowel movement, itching or a mass. Anal cancer may be easily misdiagnosed as a hemorrhoid. Anal cancer is easily detected with visual or digital examination or during anoscopy. Its extent can be assessed with endoanal ultrasound or NMR. A biopsy is needed for confirmation.  The progression of dysplasias to cancer occurs in many years, perhaps decades. Anal cancer is usually treated by combination of chemotherapy and radiotherapy. Surgery is reserved for very small lesions.

The diagnostic procedures used for diagnosis of anal HPV infection are the following:

• Visual examination of perianal skin for warts of perianal skin. Application of acetic acid (common vinegar) is mandatory when somebody looks for anal HPV infection. Acetic acid clears the mucus and precipitates nuclear proteins giving the HPV lesions a pale or dark grey color, depending on the grade of dysplasia. Warts (condylomata) are seen as small, flat lumps like lentils or small cauliflowers, their size ranging between the head of a pin to a pea. They may invade extensive surfaces in the perianal skin.
• HPV infection often extends into the anal canal. Intraanal warts and dysplasias can be diagnosed with proctoscopy and acetic acid. The anal canal is examined with a hollow tube called anoscope. Acetic acid helps in the detection of minute intraanal warts. No deeper examination is needed for assessing the HPV infection. HPV does not infect bowel lining that is 5-7 above anal verge.
• High resolution anoscopy under high magnification provides a more detailed examination of perianal skin and anal canal. Acetic acid (vinegar) application and Lugol solution is mandatory. HRA looks for minute condylomas, subclinical lesions, low grade infection of anal canal and flat premalignant HGAIN lesions.
• HPV typing– Hybrid capture or PCR are used for identification of the HPV subtype infecting anus. HPV subtypes are classified as high risk (HR-HPV) or low risk (LR-HPV). 
• Anal cytology (pap smear) is performed for screening and diagnosis of precancerous dysplasias. Pap smear should be performed in high-risk groups. Any enema or douching should be avoided before taking the test. If cytology reveals atypical cells, high resolution anoscopy under magnification should follow. High resolution anoscopy has a considerably higher diagnostic yield than anal cytology for diagnosis of preclinical precancerous dysplasias.

Any visual diagnosis of HPV infection or dysplasia (benign LGAIN or premalignant HGAIN) should be confirmed with biopsies. Koilocytes (cells with hollow nuclei), are typical of low-grade HPV infection and dysplastic cells are a typical feature in high-grade precancerous dysplasias.