A rhabdmyosarcoma is a general category that is used in the histogenetic classification of cancer to refer to a malignant neoplasm in which the malignant cells show some evidence of differentiation or determination toward the parenchymal cells found in skeletal muscle.

In general, as a result of oncogenesis, the cells comprising a cancer will have a different genotype to the constitutional genotype of the host. The genotypic changes may induce a perceptible change in the phenotype. Both of these changes may be used to classify the neoplasm. Medically useful systems of classification offer the means for diagnosis and prognosis, and may assist the physician in the choice of optimal treatment.

The cells in a particular cancer might show no overt differentiation or they might show varying degrees of differentiation that parody the appearances of some normal tissue. In a histogenetic classification, the cancer is named for the normal tissue whose phenotype is most closely mimicked. A cancer whose cells show no resemblence to any particular tissue is said to be undifferentiated. The differentiation may be perceived at the level of tissue architecture (that is, how the individual cells group together and organise themselves compared with normal tissues). An assessment of architectural relationships is the most important part of histopathology. It provides an important means to predict the biological behaviour of a neoplasm, that is, to form an opinion whether it will behave in a benign or malignant fashion. Assessment of individual cells is the main subject of cytopathology. Cytopathological assessment of cellular phenotype is best undertaken on suitably prepared whole cells that have been spread onto a glass slide. However, with some limitations, it may also be undertaken on those individual cells that form part of a neoplasm that are present in a thin section of a biopsied specimen.

Light microscopy may be used to assess the architecture of sampled tissues and the phenotype of its cells. A biopsied specimen is typically hardened and preserved in some suitable fixative. It is dehydrated and embedded in paraffin wax to allow thin sections to be taken onto glass slides. Routine assessment of these sections involves rehydration and staining with haematoxylin (which stains acidic molecules, such as nucleic acids, blue) and eosin (which stains basic molecules, such as proteins, red).

The cellular phenotype may also be assessed at the higher magnifications afforded by electron microscopy. The biopsied specimen is processed in a similar way, except that the fixatives, embedding media and stains are chosen to allow the generation of thinner sections and differential opacity to transmitted electrons rather than photons.

A change in the phenotype of a cell is effected by changes in the proteins within its cytoplasm. When this is visible using light microscopy, it may be possible to use this cellular phenotype to classify the cancer. In a rhabdomyosarcoma, the accumulation in a variable proportion of the malignant cells of large amounts of the particular isomers of the proteins that are responsible for the contractile properties of skeletal muscle typically result in large cells with cytoplasm that stains deeply red with eosin. In a small number of the malignant cells these proteins might be assembled in a structured way that imparts the "striated" appearance, characterised by alternating bands of dark and pale red, that is typical of normal skeletal muscle.

In poorly differentiated cells, the proteins that accumulate may not be present in sufficient quantities to produce a perceptible change in the appearance of the cell as judged by light microscopy. It is possible to probe for the presence of these proteins using other techniques such as immunohistochemistry. In the absence of a perceptible change in the cellular phenotype, this provides an opportunity to identify an "immunophenotype". Using this technique, the presence of proteins such as desmin, myoglobin, muscle specific actin, and others would provide strong evidence for the diagnosis of rhabdomyosarcoma.

Some cancers do not contain cells that are sufficiently differentiated to allow histogenetic classification by assessment of the cellular phenotype or immunophenotype. In some of these cells, it may be possible to identify other proteins whose presence indicates "determination" toward some particular tissue type. A cell that is "determined" has undergone modification of its genome so that the pathways of differentiation that remain open to it are restricted to those that are associated with the cells of some specific tissue. During the early stages of development of skeletal muscle cells, a protein called "myo D1" binds itself to genetic material in the cell nuclei. This is an indicator of determination towards skeletal muscle differentiation. Once skeletal muscle cells become innervated by nerve cells, the concentration of this protein falls dramatically. The same protein (myo D1) may be found in the nuclei of the cells in a rhabdomyosarcoma. As the malignant cells do not become innervated by nerve cells, this protein remains in a high concentration. This may be exploited as a means to identify malignant neoplasms that contain cells that show determination towards rhabdomyosarcoma, even when there is insufficient differentiation to allow phenotypic assessment to be used for the diagnosis. As this protein may also be present in the cytoplasm of cells of other neoplasms whose other characteristics show that they are not rhabdomyosarcomas, demonstration of the presence of myo D1 should be considered supportive for rhabdomyosarcoma only if the protein is present in the cell nuclei.