Malignant rhabdoid tumors (MRTs) are highly aggressive pediatric tumors associated with loss of expression of SMARCB1, commonly occurring in the central nervous system [referred to as atypical teratoid/rhabdoid tumors (AT/RTs)] and in the kidney and soft tissues. Histologically, MRTs are characterized by immunohistochemical evidence of primitive neuroectodermal, mesenchymal, and epithelial differentiation. The ability of MRTs to differentiate along multiple lines, as evidenced by both histologic features and polyphenotypic immunohistochemical staining, and the proliferative nature of MRT cells are characteristics shared with the self-renewal and plasticity of embryonic stem cells (ES). To test the hypothesis that MRTs share similarities with ES, we used immunohistochemistry to evaluate the expression of various stem cell markers in a tissue microarray containing 26 AT/RTs and 16 non-central nervous system MRTs (NCMRTs). Staining intensity was scored as negative (0), low (1+), moderate (2+), and strong (3+) and was multiplied by the percentage of positive tumor cells to establish a semiquantitative measure for each marker. In AT/RT, strong-to-low expression was noted with glypican-3 (20 of 26, 77%), Sall4 (23 of 26, 88%), T-cell leukemia/lymphoma 1 (25 of 26, 96%), and undifferentiated embryonic cell transcription factor 1 (19 of 26, 73%). Markers that showed low expression in AT/RT were Sox2 (8 of 26, 31%), Nanog (7 of 26, 27%), Klf4 (10 of 26, 38%), Zfp206 (5 of 26, 19%), and musashi-1 (21 of 26, 81%). Similarly, in NCMRT, expression was noted with glypican-3 (12 of 16, 75%), Sall4 (13 of 16, 81%), T-cell leukemia/lymphoma 1 (16 of 16, 100%), undifferentiated embryonic cell transcription factor 1 (12 of 16, 75%), Sox2 (5 of 16, 31%), Nanog (8 of 16, 50%), Klf4 (8 of 16, 50%), Zfp206 (13 of 16, 81%), and musashi-1 (11 of 16, 75%). Placental alkaline phosphatase, Oct4, c-KIT, CD30, α-fetoprotein, and β- -human chorionic gonadotrophin were not expressed in all cases. Markers that regulate the expression of stem cell transcription factors were also expressed in MRT. AT/RT cases showed expression of Id proteins: Id1 (17 of 26, 65%), Id2 (24 of 26, 92%), Id3 (22 of 26, 85%), and Id4 (22 of 26, 85%). Low expression was observed with EZH2 (15 of 26, 58%). Similarly, NCMRT cases showed expression of Id1 (15 of 16, 94%), Id2 (16 of 16, 100%), Id3 (16 of 16, 100%), Id4 (13 of 16, 81%), and EZH2 (13 of 16, 81%). Finally, regression analysis revealed a significant relationship between the expression of stem cell markers and EZH2 (P<0.0001), Id1 (P=0.0087), Id2 (P=0.0002), Id3 (P=0.0033), and Id4 (P<0.0001). These data suggest that MRTs express many stem cell-associated transcription factors, which may be regulated by the expression of EZH2 and the Id family of proteins. This study underscores similarities between MRTs and stem cells and may help elucidate common biologic pathways that could serve in advancing more effective therapeutic strategies to treat MRTs.