Poorly differentiated malignancies affecting the anal canal are uncommon but pose diagnostic difficulties because of the wide range of normal cell types that may occur within a limited anatomical region. The range of lesions that may present as poorly differentiated tumours includes squamous cell carcinoma, adenocarcinoma, small and large cell neuroendocrine carcinoma, neuroendocrine carcinoma expressing epithelial cytokeratins and other patterns of mixed differentiation, undifferentiated carcinoma, malignant melanoma, lymphoma and secondary tumours. This review discusses the differential diagnosis of these neoplasms with the aid of short illustrative case studies.