Squamous cell carcinoma of the anus (SCCA) is a rare disease, but its incidence has been increasing dramatically since the 1970s. Men who have sex with men (MSM) and infection with human immunodeficiency virus (HIV) are the two main risk factors. Risk of developing SCCA is increased more than 100-fold in HIV-seropositive MSM. We review here how immunodeficiency could promote SCCA and how restoration of immunity since the advent of combined antiretroviral therapy can influence the natural history and incidence of SCCA. We also review the prognostic and therapeutic implications of immunosuppression in these patients. Finally, we show how, with anti-HPV vaccines, immunity is a target in the prevention of SCCA and could in the future be used in its treatment.