Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood with presumed origins of skeletal muscle because of its myogenic phenotype. RMS is composed of two main subtypes, embryonal RMS (eRMS) and alveolar (aRMS). While eRMS histologically resembles embryonic skeletal muscle, the aRMS subtype is more aggressive and exhibits a poorer prognosis. In addition, whereas the genetic profile of eRMS is less established, aRMS is commonly associated with distinct chromosome translocations that fuse domains of transcription factors, Pax3 or Pax7 to FKHR (Foxo1A). Both eRMS and aRMS tumor cells express myogenic markers such as MyoD, but their ability to complete differentiation is impaired. How this impairment occurs is the subject of this review, which will focus on several themes that include signaling pathways that converge on Pax-FKHR gene targets, alterations in MyoD function, epigenetic modifications of myogenic promoters, and microRNAs whose expression patterns in RMS alter key regulatory circuits to help maintain tumor cells in an opportunistically less differentiated state.