Atypical teratoid/rhabdoid tumor (AT/RT) and dedifferentiated/poorly differentiated chordoma are pediatric tumors with some overlapping morphologic, immunohistochemical, and molecular features. Both these tumors have alterations in the tumor suppressor gene SMARCB1 resulting in loss of expression of the INI-1 protein. On the contrary, dedifferentiated/poorly differentiated chordoma expresses the transcription factor brachyury, whereas AT/RT does not. In this article we have reviewed the clinicopathologic features of a pediatric series of tumors (17 samples from 14 patients) located in the brain or within the axial spine and the base of the skull diagnosed as AT/RTs or as dedifferentiated/poorly differentiated chordomas. On the basis of the INI-1 and brachyury immunohistochemical results we reevaluated the initial diagnoses. Four misdiagnoses were revised. The differential diagnosis between AT/RT and dedifferentiated/poorly differentiated chordoma or on occasion medulloblastoma may be difficult. The use of 2 antibodies, INI-1, and brachyury, may be the key for the right diagnosis.