Alveolar rhabdomyosarcoma may be extremely difficult to distinguish from other primitive round cell neoplasms without ancillary immunohistochemistry and/or genetic study. Particularly in adults and in the head and neck locations, the differential diagnosis of alveolar rhabdomyosarcoma includes small cell carcinoma and neuroepithelial tumors, such as esthesioneuroblastoma. We have recently seen cases of genetically confirmed alveolar rhabdomyosarcoma, which were misdiagnosed owing to expression of cytokeratins and neuroendocrine markers. We studied a large group of well-characterized alveolar rhabdomyosarcomas for expression of such markers. Forty-four alveolar rhabdomyosarcomas (18 genetically confirmed) were retrieved from our archives and immunostained for wide-spectrum cytokeratin (OSCAR), low molecular weight cytokeratin (Cam5.2), synaptophysin, chromogranin A, and CD56 using commercially available antibodies. Cases were scored as 'negative', 'rare' (<5% positive cells), '1+' (5-25%), '2+' (26-50%) and '3+' (>51%). The tumors occurred in 23 males and 21 females at a mean age of 18 years (range, <1-64 years), and involved many sites. Fifty percent of cases (22 of 44) expressed wide-spectrum cytokeratin, and scored almost equally as rare, 1+, and 2+, but rarely 3+. Cam5.2 was positive in 52% (14 of 27). Forty-three percent of cases (16 of 37) expressed at least one of the specific neuroendocrine markers, 32% (12 of 37) expressed synaptophysin, 22% (eight of 36) expressed chromogranin A, and 11% expressed both. Expression of synaptophysin and chromogranin A was typically confined to rare cells but could be more widespread. Thirty-two percent of cases (12 of 37) expressed the wide-spectrum cytokeratin and at least one of the neuroendocrine markers, and 8% (three of 36) expressed cytokeratin and both neuroendocrine markers. CD56 expression was nearly ubiquitous. Aberrant expression of epithelial and neuroendocrine markers is relatively common in alveolar rhabdomyosarcoma, occurring in 30-40% of cases. These findings have significant implications for the diagnosis of alveolar rhabdomyosarcoma, particularly in adults and in the head and neck locations. Although expression of cytokeratin and/or synaptophysin alone does not necessarily indicate epithelial or neuroendocrine differentiation, coexpression of cytokeratin and neuroendocrine markers, and in particular the presence of chromogranin expression, suggest true epithelial and/or neuroendocrine differentiation in a subset of alveolar rhabdomyosarcomas. CD56 is not a specific neuroendocrine marker, and should not be used in the absence of synaptophysin/chromogranin. These findings emphasize the need to employ a panel of markers, to include desmin, myogenin/MyoD1, and genetic study in the diagnosis of primitive round cell neoplasms in all age groups and in all locations.