Malignant rhabdoid tumors (MRTs) are a group of highly malignant and highly aggressive embryonic tumors that tend to occur in infants and young children. According to primary locations, childhood MRTs are classified into atypical teratomoid/rhabdoid tumors of the central nervous system (AT/RT), malignant rhabdoid tumor of the kidney (MRTK) and extrarenal extracranial rhabdoid tumor (EERT). The deletion of SMARCB1 gene and loss of its encoded protein INI 1 are the driving genetic defects and important diagnostic evidence of MRTs in children. The prognosis of MRTs in children is poor, and the overall survival rate is only about 40 % even after the combined treatment of surgery, radiotherapy, chemotherapy and autologous hematopoietic stem cell transplantation. This article reviews the progress of abnormal molecular genetics and targeted therapy of MRTs in children.