Anal canal cancer is rather an uncommon disease but its incidence is increasing. Squamous cell carcinoma (SCC) is the most frequent primary anal neoplasm and can encompass a variety of morphologies. HPV infection has a key role in precancerous lesions and cancer development by the production of E6 and E7 oncoproteins. Anal squamous precancerous lesions are now classified according to the same criteria and terminology as their cervical counterparts. The p16 expression by immunohistochemistry is a surrogate marker for human papilloma virus (HPV). Many other tumor types can arise in the anal canal, including adenocarcinomas, neuroendocrine tumors, malignant melanomas, lymphomas and various types of mesenchymal tumors. For differential diagnosis, immunostaining markers such as CK5/6 and p63 can be used to distinguish SCC and CK7 for adenocarcinoma. Other classical panels can also be applied as in other locations. Currently, there are no biomarkers able to predict prognosis or response to treatment in clinical practice.