To understand the molecular pathogenic mechanism of PAX3-FKHR in the development of RMS, we used ChIP-seq to map PAX3-FKHR genomic binding sites associated with 1072 genes in RMS cells. I. The data shows that PAX3-FKHR binds to the same sites as PAX3 at enhancers for MYF5, FGFR4, as well as the MYOD core enhancer previously shown to be downstream of PAX3 regulation. Moreover, our dataset has the precision for a rapid identification and validation of novel and specific sequences required for the enhancer activity for MYOD and FGFR4. II. The genome wide analysis reveals that the vast majority of PAX3-FKHR sites are: 1) distal to transcription start sites; 2) conserved; 3) enriched for PAX3 motifs; 4) strongly associated with genes over-expressed in PAX3-FKHR positive RMS cells and tumors. There is little evidence in our dataset for PAX3-FKHR binding at the promoters. In one instance, our data establishes two intronic enhancer elements for MET, rather than at the previously described promoter. The genome-wide analysis further illustrates a strong association between PAX3 and E-box motifs in these binding sites, suggestive of a common co-regulation for many target genes. III. The map of PAX3-FKHR binding sites provides new links for PAX3 and PAX3-FKHR functions and new targets for RMS therapy. Our study identifies genes that are critically important for different aspects of limb-genesis, as direct PAX3-FKHR targets. Further, we identify IGF1R as a direct target for PAX3-FKHR. The dependence on IGF1R for survival in some RMS cells with PAX3-FKHR makes it an ideal therapeutic target for this cancer.