Renal rhabdoid tumor (RRT) is the most malignant and aggressive renal tumors in children. The results of immunohistochemistry show co-expression of epithelial and mesenchymal markers with total loss of INI1 expression in tumor cells. Aim. To determine the frequency of WT1 expression in RRT using three different clones and to investigate WT1 gene status. This study is supported by the Independent Ethics Committee and approved by the Academic Council of the Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology. 28 patients with RRT were included in our study from a period 2006–2019. Immunohistochemical staining included Vimentin, panCK, CK19, EMA, INI1, CD34, WT1 (clones: polyclonal, WT49, 6FH2). Additionally, in order to evaluate genetic events known to be significant in the RRT pathogenesis, molecular genetic testing by multiplex ligase-dependent probe amplification (NGS) and next-generation sequencing (NGS) of customized gene panel were conducted in 15 cases with available material. All tumors had classical rhabdoid morphology with co-expression of epithelial and mesenchymal markers and total loss of INI1 expression. Two tumors were WT1-positive (WT49 and Polyclonal). 5 out of 15 tumors harbored different in length SMARCB1 gene deletions. 7 cases studied by NGS for nucleotide substitutions and small indels included 5 patients lacking SMARCB1 deletions based on the MLPA data and 2 cases of RRT with WT1 protein nuclear expression. All evaluated patients had pathogenic or likely-pathogenic genetic variants in genes encoding core subunits of SWI/ SNF chromatin remodeling complex (predominantly, SMARCB1 and SMARCA4 genes). No pathogenic variants were revealed in WT1 gene. The literature describes isolated cases of WT1 expression in RRT elements. Often, the cellular elements of a rhabdoid tumor after preoperative chemotherapy are regarded as elements of the stromal component of nephroblastoma, maturing into rhabdomyoblasts. In the presence of WT1 expression, these tumors are considered as nephroblastomas. In this study we showed that RRTs are molecularly heterogeneous tumors with aberrant immunophenotype. Thus, our experience proves the importance of an integrated approach to differential diagnosis and the need for routine use of the INI1 antibody in panels for the study of kidney tumors in children to avoid misinterpretation of morphological data.