Embryonal rhabdomyosarcoma is a rare cancer that often requires multimodality therapy to treat; however, these therapies can cause changes in the biology of the tumor. Several reports have documented pathologic changes but only recently have genetic changes been mapped. We present case of two separate synchronous primary rhabdomyosarcomas in a 17-month-old patient and discuss the pathophysiology and genetic changes that occur with treatment. We hypothesize that a genetic field defect arising in development of the urogenital sinus caused the tumors, but that treatment modalities may have caused genetic alterations changing clinical behavior of the tumors and responses to treatment.