Abstract: Two histopathologically different kinds of rhabdomyosarcoma (RMS) -alveolar and embryonal RMS- are associated with distinct clinical characteristics and different cytogenetic properties. Affymetrix microarrays (U133A/B) were used to characterize the 74 tumoral tissues of both kinds. For consistency with previous work, 8801 genes have been considered in our analysis. Also, the train/test division had been fixed to 56 training and 18 test data. Feature Selection (FS) is both useful for enhancing the classification performance and, more importantly, to discover biologically relevant genes. Therefore, FS is a hot topic in the application of machine learning to the analysis of microarray data.