Malignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive Schwann cell neoplasms that are frequently associated with Type I Neurofibromatosis (NF1) and respond poorly to current therapeutic regimens. To better understand the molecular heterogeneity of these tumors, we performed gene expression profiling on 25 NF1-associated and 17 sporadic MPNSTs using oligonucleotide microarrays representing approximately 8100 unique human gene transcripts. Using several previously reported statistical approaches, we were unable to identify a molecular signature that could reliably distinguish between NF1-associated and sporadic MPNSTs in independent training and test sample sets. However, using an unsupervised clustering approach, we identified an extensive gene expression signature that distinguished 9 of the 42 tumors analyzed. This signature corresponded to relative overexpression of transcripts associated with neuroglial differentiation (NCAM, MBP, L1CAM, P1P) and relative down-regulation of proliferation and growth factor associated transcripts (IGF2, FGFR1, MDK, Ki67). All tumors with this gene expression signature lacked expression of EGFR and all but one tumor were derived from patients with NF1. However, there were no other obvious associations with histological grade, tumor site, metastasis, recurrence, age, or patient survival. We conclude that distinct molecular classes of MPNST exist and that the ability to stratify these tumors based on unique and biologically relevant gene expression profiles may be important for future targeted therapeutics.