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Malignant rhabdoid tumors (MRT) are characterized by unique neoplastic cells demonstrating phenotypic diversity. By using the reverse transcriptase-polymerase chain reaction, we have detected expression of various genes before and after differentiation induction with four different agents in four established MRT cell lines (TM87–16, STM91–01, TTC642, and TTC549). The agents used in this study were all-trans retinoic acid (RA), 12-O-tetradecanoylphorbol-13-acetate (TPA), interleukin-3, or interferon-gamma. Before and after induction, c-myc, IGF-II, IGF-I receptor, and IGF-II receptor were constitutively expressed by all four cell lines. The neurofilament medium-size (NF-M) was constitutively expressed by the TM87–16 and TTC642, and the S100 protein alpha subunit was expressed by TM87–16, TTC642, and TTC549. Chromogranin A was expressed by TM87–16 only after treatment with either TPA or RA. MyoD, N-myc, tyrosine hydroxylase, N-CAM, trkA, and the S100 protein beta subunit were not expressed by any cell line before or after induction with these agents. All the MRT cell lines in this study except TM87–16 were highly resistant to differentiation induction. The proliferating cells in TM87–16 and TTC642 expressed mRNA profiles characteristic of neuroectoderm.