Currently, it is recognized that there is an HPV-related and an HPV-independent pathway to developing squamous cell carcinomas (SCC) in the anus and vulva. The majority of precursor lesions and SCC in the anus and vulva are high-risk HPV-associated, with HPV16 the most common type. Given the morphologic overlap and biological equivalence of HPV-related preinvasive squamous lesions of the lower anogenital tract, a unified, 2-tiered histopathologic nomenclature is now recommended. In contrast, mutations in the TP53 gene have been associated with HPV-independent vulvar and anal SCC. A precursor lesion—differentiated or simplex vulvar intraepithelial neoplasia (dVIN)—has been identified for HPV-independent vulvar SCC but a similar lesion in the anus has not been described. Extramammary Paget disease is a nonsquamous intraepithelial lesion of the vulva and anus that may be a primary epidermotropic apocrine neoplasm or may represent secondary involvement by a synchronous/metachronous adenocarcinoma. This entity may be mimicked by squamous lesions and melanocytic lesions. Herein, we discuss the morphologic and immunohistochemical features of anal and vulvar intraepithelial neoplasia in the context of updated terminology and current understanding of disease biology.