cDNA microarrays allow large-scale analysis of the effects of oncogenic transcription factors on gene expression. Alveolar rhabdomyosarcoms (ARMS) are aggressive soft tissue tumours of striated muscle in which 60% have a reciprocal translocation involving chromosomes 2 and 13, [t(2;13)(q35;q14)]. This results in a novel fusion transcription factor, PAX3-FKHR. Using retroviral transduction we have introduced both PAX3 and PAX3-FKHR into NIH3T3 cells and used a mouse cDNA microarray containing 2,200 elements to investigate their effects on gene expression. Introduction of PAX3-FKHR resulted in increased expression of several genes, including that encoding the myogenic transcription factor myogenin, as well as other muscle-specific genes. In contrast, PAX3 failed to induce these genes and repression of several genes was noted, some of which were also downregulated by PAX3-FKHR. This study demonstrates the potential of cDNA microarrays to elucidate the pathways of malignant transformation by oncogenic transcription factors.