Primary intraosseous rhabdomyosarcomas are extremely rare. Recently two studies reported 4 cases of primary intraosseous rhabdomyosarcoma with EWSR1/FUS-TFCP2 gene fusions, associated with somewhat conflicting histologic features, ranging from spindle to epithelioid. In this study we sought to further investigate the pathologic and molecular abnormalities of a larger group of intraosseous rhabdomyosarcomas by a combined approach using targeted RNA sequencing analysis and fluorescence in-situ hybridization (FISH). We identified 7 cases, 3 males and 4 females, all in young adults, age range 20-39 years (median 27 years). Three cases involved the pelvis, 2 involved the femur and 1 each involved the maxilla and the skull. Molecular studies identified recurrent gene fusions in all 7 cases tested, including: a novel MEIS1-NCOA2 fusion in 2 cases, EWSR1-TFCP2 in 3 cases and FUS-TFCP2 gene fusions in 1 case. One case showed a FUS gene rearrangement, without a TFCP2 gene abnormality by FISH. The MEIS1-NCOA2 positive cases were characterized by a more primitive and fascicular spindle cell appearance, while the EWSR1/FUS rearranged tumors had a hybrid spindle and epithelioid phenotype, with more abundant eosinophilic cytoplasm and mild nuclear pleomorphism. Immunohistochemically, all tumors were positive for desmin and myogenin (focal). In addition, 4 tumors with TFCP2 associated gene fusions also co-expressed ALK and Cytokeratin. In conclusion, our results suggest a high incidence of gene fusions in primary rhabdomyosarcomas of bone, with two molecular subsets emerging, defined by either MEIS1-NCOA2 or EWSR1/FUS-TFCP2 fusions, showing distinct morphology and immunophenotype. Additional studies with larger numbers of cases and