Malignant rhabdoid tumor (MRT) is considered to display multi-phenotypic characteristics but the true origin of this tumor remains unknown. In recent years, the concept of the cancer stem cell (CSC) has drawn great attention. In the present study we investigated six MRT cell lines (TM87-16, STM91-01, TTC642, TTC549, YAM-RTK-1 and TTC1240), for CD133, nestin and Musashi-1 (Msi-1), which are considered to be CSC as well as neural stem cell (NSC) markers, using assays for cell viability and apoptosis, reverse transcriptional polymerase chain reaction (RT-PCR), semi-quantitative PCR and Western blot analysis before and after differentiation-induction with N-(4-hydroxyphenyl) retinamid (4-HPR). Before differentiation-induction with 4-HPR, CD133 was detected in three MRT cell lines, nestin in three cell lines and Msi-1 in five cell lines. In TTC549 after differentiation-induction with 4-HPR, nestin and Msi-1 were down-regulated in a time-dependent manner. Similar down-regulation of Msi-1 was recognized in YAM-RTK-1. In STM91-01, CD133 was gradually down-regulated and Msi-1 was down-regulated after a transient increase. Results from our study indicated that 4-HPR might be effective in some MRTs. Expression of NSC markers showed that some MRTs contain a subpopulation of NSC and down-regulation of NSC markers in MRT cells provides supportive evidence that many MRTs could be considered of neuroectodermal origin.