The International Classification of Rhabdomyosarcoma (ICR) has provided diagnostic criteria for rhabdomyosarcoma (RMS) and formed the basis of histologic risk stratification since its publication in 1995. However, the recognition of new variants of embryonal rhabdomyosarcoma (ERMS), shifts in the diagnostic criteria of alveolar rhabdomyosarcoma (ARMS), the increasing use of myogenin immunohistochemistry and recognition of the distinct biologic properties associated with fusion status all raised questions about the continued use of this classification system in the diagnosis and treatment of patients with RMS. Recent Children's Oncology Group Soft Tissue Sarcoma Committee analysis of histology and fusion status in the intermediate risk RMS study D9803 refined the histologic criteria of RMS. We validated the new diagnostic criteria against fusion status, allowing prospective examination of the prognostic value of histology compared with fusion status for risk-stratification of patients with RMS. This article summarizes the evolution of and current practices in the histologic and molecular classification of rhabdomyosarcoma.