This study presents a case of embryonal rhabdomyosarcoma (ERMS) of the forearm soft tissue in a 12-year-old female, in which microtubular aggregates in rough endoplasmic reticulum (rER) were noted ultrastructurally. Histologically, tumor cells consisted of typical rhabdomyoblastoid cells with abundant eosinophilic cytoplasm and relatively immature, small tumor cells. Ultrastructurally, two different types of tumor cells were also identified by light microscopy. More than half the tumor cells possessed the characteristic features of rhabdomyoblastic differentiation, such as abundant thick and thin filaments with Z-bands. The other tumor cells were less differentiated cells in which microtubular aggregates (MA) in rER were observed. MA in rER have been described in several nonepithelial tumors, including malignant melanoma, osteosarcoma, extraskeletal myxoid chondrosarcoma, and chordoma. ERMS is another example of mesenchymal tumor in which MA in rER are observed by electron microscopy. Considering the differential diagnosis among mesenchymal tumors, it is important to know that MA can be also observed in ERMS.