The presence, morphology and distribution of anal neuroendocrine cells were investigated with a panel of antisera and antibodies for neural markers, biogenic amines, and neuropeptides by the sensitive streptavidin-biotin-peroxidase immunocytochemistry, and coexistence patterns of neurochemically characterized neuroendocrine cells were examined by double immunofluorescence cytochemistry. In the colorectal zone, endocrine-like cells were immunoreactive for chromogranin A (CGA), serotonin (5-HT), pancreastatin (PST), peptide tyrosine tyrosine (PYY), glucagon-like peptide-1 (GLP-1), and somatostatin (SOM). Coexistence patterns of endocrine-like cell phenotypes with CGA and GLP-1 were heterogeneous. In the anal transitional zone (ATZ), endocrine-like cells were immunoreactive for CGA, 5-HT and PST. Furthermore, six new phenotypes of endocrine-like cells were characterized by their immunoreactivity for PYY, GLP-1, protein gene product 9.5 (PGP), calcitonin gene-related peptide (CGRP), neurotensin (NT), and SOM. All endocrine-like cell types in the ATZ were immunoreactive for CGA. In the squamous zone and perianal skin, CGA-immunopositive Merkel cells were also immunoreactive for CGRP, PST, NT and PGP. Neuroendocrine cells in the anal canal exhibit epithelial zone-related diversities in their neurochemical phenotypes and coexistence patterns, which may indicate specific regulatory functions. In the epithelium of the ATZ, which is regarded as metaplastic, endocrine-like cells expressed phenotypes characteristic of the neuroendocrine cells of the colorectal zone and the squamous zones, indicating a possible metaplastic origin of these cells.