Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal tumors of the intestinal tract. In patients with locally advanced and/or metastatic GIST, the introduction of tyrosine kinase inhibitor, imatinib mesylate, has transformed the management of this previously untreatable neoplasm into a treatable entity. Approximately 80% of advanced metastatic GISTs respond to imatinib treatment. However, the majority of patients suffer disease progression at a median of 2 years due to drug resistance. Generally progressing GISTs retain their typical morphology. Herein, we report an extremely rare case of progressive metastatic GIST with heterologous rhabdomyoblastic differentiation after, imatinib mesylate treatment. We also review the relevant literature.