Stages of anal cancer are indicated using Roman numerals ranging from 0 to IV, with earlier stage cancers such as stage I and II are more likely to be cured than more advanced stages with larger tumors and cancers that have spread to local lymph nodes.

The goal of CMT is to eradicate the tumor and still preserve the anus.

Using combined modality therapy, the anal sphincter can be preserved in a majority of patients. Even cancers that have spread to the lymph nodes can have good results. Prognosis can also depend on location of the tumor whether it is located in the anal canal versus the anal margin or perianal skin. Locally advanced tumors greater than 5 cm (T3), tumors of any size that invade adjacent organ such as the vagina, urethra, or bladder (T4), lymph node involvement can also affect prognosis. 

Another factor that can affect prognosis is being HIV-positive, particularly for patients with CD4 lymphocyte counts under 200.

Up to 90% of patients present with local disease without distant metastases. Sometimes the cancer may return in the original site also known as a local recurrence which mostly happens within the first 2 years of completing therapy. When local recurrences occur after CMT, patients may need to undergo the APR procedure and approximately 50% of patients will be cured with this additional operation.