Ultrastructural analysis of the skeletal muscle cells in adult-onset Pompe disease revealed lysosomal and cytoplasmic glycogen storage, autophagic vacuoles and abnormal mitochondria. Significant glycogen accumulation within lysosomes causes their rupture and release of glycogen into the cytoplasm. Excess cytoplasmic glycogen could lead to damage of the structure of muscle cells including myofibrils. In consequence, parts of the sarcoplasm and damaged organelles were sequestered within membrane-limited vacuoles. We suppose that massive accumulation of autophagic vacuoles results from the inability of destroyed lysosomes to fuse with vacuoles. Autophagic vacuoles may be a prominent feature of muscle cells in adult glycogenosis type II.