The introduction and application of molecular techniques have commenced to influence and alter the nosology of congenital myopathies. Long-known entities such as nemaline myopathies, core diseases, and desmin-related myopathies have now been found to be caused by unequivocal mutations. Several of these mutations and their genes have been identified by analyzing aggregates of proteins within muscle fibers as a morphological hallmark as in desminopathy and actinopathy, the latter a subtype among the nemaline myopathies. Immunohistochemistry has played a crucial role in recognizing this new group of protein aggregate myopathies within the spectrum of congenital myopathies. It is to be expected that other congenital myopathies marked by inclusion bodies may turn out to be such protein aggregate myopathies, depending on analysis of individual proteins within these protein aggregates and their association with putative gene mutations.