Sarcomas represent a considerable diversity, they are widely conflicting family of cancers that arise in mesenchymal tissue. They are highly aggressive cancers that can progress in any part of the body and about 10% of sarcomas appear around the head and neck. The most common type of bone sarcomas are osteosarcoma. The most common soft tissue sarcoma in children is rhabdomyosarcoma. CD44 is a type I transmembrane glycoprotein that is widely expressed as cell surface adhesion molecule on many types of cells. CD44 supports the migration of metastatic cells from the site of primary tumor growth to remote organs. Recent studies have implicated CD44 in the invasion, metastasis and progression of several human cancers. Our goal was the detection of CSCs in the most common oral sarcomas (osteosarcoma and rhabdomyosarcoma) by anti CD44 antibody as a stem cell marker using immnunohistochemical and immunofluorescence techniques. Results: Both techniques showed that CD44 immunoexpression in rhabdomysarcoma exceeded that of osteosarcoma. The area percentage of CD44 positive cells and its optical density showed a highly statistically significant difference between rhabdomysarcoma and osteosarcoma using Student’s t test. Conclusion: CSCs are identified in osteosarcoma and rhabdomyosarcoma using CD44, which could be used as a potential CSC as well as prognostic marker in those lesions. Increased CD44 immunoreactivity of rhabdomyosarcoma over osteosarcoma could be indicative for more aggressive behavior. Fibroblastic osteosarcoma and alveolar rhabdomyosarcoma could be more aggressive subtypes than the other examined ones.