Summary Anal canal pathology, particularly infections and tumours, has recently come into prominence, mainly because of human immunodeficiency virus (HIV) and acquired immunodeficiency syndrome. This review provides a framework for diagnostic pathologists who may encounter anal canal tumours. A summary of embryology, anatomy and terminology is provided by way of background. Important points of distinction between the surgical, anatomic and histologic anal canal are highlighted. Squamous carcinomas and their precursor lesion, anal intra-epithelial neoplasia, are the most common primary epithelial abnormalities seen in the anal canal. In addition, there is a predilection for HIV-positive homosexual men with co-existent human papillomavirus (HPV) infection to develop squamous carcinomas. The more proximal the tumour is in the anal canal, the greater the association with basaloid morphology and HPV infection. Adenocarcinomas are uncommon and may arise from the anal transitional zone, anal glands or fistulous tracts, which may or may not be associated with long-standing Crohn's disease. The immunohistochemical profiles and separation from morphologically similar tumours are provided in this article. In addition, the role of new molecular markers is discussed in relation to tumour behaviour and therapeutic options.