The diagnosis of malignant rhabdoid tumor (MRT) is straightforward if the typical, large eosinophilic rhabdoid cells are identified. We report on two diagnostically challenging cases of pediatric extra-renal MRTs which, when evaluated at incisional biopsy, were composed exclusively of small- to medium-sized round cells with focal spindling, lacking rhabdoid phenotype. This morphology, along with a polyphenotypic immunoprofile, including the expression of vimentin/CD99/cytokeratins/alpha-smooth muscle actin and vimentin/CD99/S-100 protein in case 1 and case 2, respectively, suggested the possibility of Ewing sarcoma (EWS)/PNET. However, molecular analyses failed to show the presence of the EWS/FLI-1 and EWS/ERG fusion transcripts, indicative of the most common translocations, i.e., t(11;22)(q24;q12) and t(22;21)(q22;q12), occurring in this tumor family. The revision of both cases included an immunohistochemical analysis with a commercially available anti-INI1 protein antibody. Immunohistochemistry, showing the absence of INI1 expression in neoplastic cells, strongly supported the diagnosis of MRT. Ultrastructural studies, performed on formalin-fixed tissues, were consistent with the diagnosis of MRT. This study suggests including anti-INI1 protein antibody in the immunohistochemical panel when evaluating pediatric tumors with ambiguous morphological and immunohistochemical features, particularly from small biopsies. A careful evaluation of clinical, pathological, and molecular findings is the key to a correct diagnostic approach of pediatric tumors.