Objective: To evaluate the expression and clinicopathological significance of epithelial and neuroendocrine markers: cytokeratin (CK), synaptophysin (Syn), chromogranin A (CgA) in rhabdomyosarcoma of children. Methods: A retrospective analysis of 56 cases of rhabdomyosarcoma was made. Immunohistochemical method was used to detect the expression levels of CK, Syn and CgA in rhabdomyosarcoma tissues of various types, and the follow-up results was analyzed. Results: There were 38 males and 18 females with an average age of 3 years and 11 months. Location of occurrence: urogenital tract was the most common (16/56, 28.6%). Microscopically, 32 cases of embryonic rhabdomyosarcoma, 19 cases of alveolar rhabdomyosarcoma and 5 cases of spindle cell rhabdomyosarcoma were diagnosed in 56 cases. Immunophenotype: 41.1% (23/56) of patients expressed CK, 43.1% (22 of 51) expressed Syn, and 22.4% (11/49) expressed CgA; the expression of syn and CgA was localized, and 22% expressed both. CK and Syn or CgA were expressed simultaneously in 9% of cases. Conclusion: These epithelial and neuroendocrine markers can be expressed to varying degrees in various types of RMS. This finding highlights the need to employ a panel of markers to diagnose and differentiate rhabdomyosarcoma from neuroendocrine tumors and other small round cell tumors.