Various methods of muscle biopsy morphological analysis are very important in the differential diagnostics of congenital myopathies. Not all neuromuscular diseases are identified by clear diagnostic criteria of morphological changes. The aim of this study was to search for electron microscopic markers, effective for the differential diagnosis of central core myopathy. Muscle biopsies were investigated in 56 patients aged from 1 to 21 years with diagnosis of central core myopathy (24 patients), multicore disease (6 patients), sarcotubular myopathy (10 patients), mitochondrial myopathy (16 patients). There were used methods of light (including histochemical) and electron microscopy. There were revealed basic electron-microscopic characteristics that could be used for differential diagnosis of congenital myopathies: central core, multicore and sarcotubular myopathies, as well as their morphological differences from mitochondrial myopathies.