Abstract Paget's disease of the anus is a rare disorder of controversial origin and is frequently associated with malignancy. We studied eight patients and carried out immunohistochemical studies to determine whether particular functional profiles might be indicators of a malignant association. One patient presented with synchronous carcinoma and two developed carcinomas 3 and 10 years after excision of Paget's disease. Five patients underwent wide local excision and have not developed cancer (median follow-up 6 years, range 5-13 years). However, four patients developed recurrent Paget's disease. Immunohistochemical studies showed that in general Paget cells stained positively with CAM 5·2 (a cytokeratin marker), gross cystic disease fluid protein (a marker for apocrine cells), human milk fat globule glycoprotein (HMFG 1 and 2) and carcinoembryonic antigen but negatively for PR3A5 (a marker for colonic goblet cells). Three cases had a staining profile which was quite different from that usually observed and these were associated with malignancy. One showed an antigenic profile more typical of a large bowel carcinoma. Paget's disease of the anus appears to run one of two clinical courses: to develop malignancy; or to recur locally, often on repeated occasions. Wide local excision is the treatment of choice but long-term follow-up is necessary because of the cancer risk. An immunohistochemical staining pattern which is different from usual may indicate a higher malignant risk and/or identify some cases of Paget's disease as representing a downward ‘pagetoid’ extension from a anorectal adenocarcinoma rather than a true epidermotropic apocrine neoplasm of the perianal skin.