Extramammary Paget's disease (EMPD) is a rare condition whose importance is amplified by its association with either cutaneous or internal malignancy. Recently it has been shown that EMPD is not a single disease but can be divided into cutaneous and endodermal subtypes. The authors studied 12 new cases of immunohistochemically well-characterized EMPD, including HER-2/neu and CDX-2 immunophenotyping. The latter represents a novel application of this nuclear transcription factor, considered to be a relatively specific IHC marker for gastrointestinal-type epithelium. Cutaneous EMPD, accounting for 10 of the 12 (83%) cases, was CDX2-/HER2+; endodermal EMPD, accounting for 2 of the 12 (17%) cases, was CDX2+/HER2-. Four of the 12 cases (33%) were associated with a malignancy (two cutaneous adenocarcinomas, two colorectal carcinomas). The two cases of cutaneous adenocarcinoma occurred in the cutaneous group (2/10 [20%]), while the two cases of rectal carcinoma (one invasive, one in situ) occurred in the endodermal group (2/2 [100%]). Since EMPD subtypes have specific implications with regard to cancer risk, immunophenotyping should be performed in all cases. CDX-2 immunoreactivity may be useful in the subtyping of EMPD.