Squamous cell carcinoma (SCC) of the anus, an increasingly prevalent malignancy, can be cured with chemotherapy and radiation alone in 50–70 % of cases. Nonoperative therapy avoids a permanent colostomy, but up to 20 % of all patients with SCC of the anus require abdominoperineal resection (APR) and a stoma. The likelihood of cure is higher for smaller tumours (<5 cm) compared to larger and deeply invasive tumours. Anal cancer recurrence is most commonly local; distant metastases affect only 10–15 % of patients. Recent innovations have included improved imaging techniques such as endoanal ultrasound, magnetic resonance imaging (MRI) and fluorodeoxyglucose positron emission tomography (FDG-PET) for pretreatment clinical staging as well as posttreatment follow-up. Intensity-modulated radiation therapy (IMRT) is also emerging as a more precise modality for targeting radiation therapy, with reported decreased rates of toxicity. Prospective data on this technique is still pending. Patients with persistent or recurrent SCC of the anus after chemoradiation are candidates for salvage APR, a major resection that may involve en bloc resection of contiguous organs (vagina, bladder, prostate). Other rare malignancies of the anus include adenocarcinoma and melanoma. Anal adenocarcinoma patients have a 40–50 % 5-year survival, with many patients developing distant metastases. Many authors believe that chemoradiation followed by surgical resection is the best treatment approach for those without metastases at presentation. Anal melanoma has a poor survival, with frequent inguinal node and distant metastases. Most authors recommend wide local excision as opposed to APR, and chemotherapy options are poor.