The effects of heavy ion microbeams on muscle fibers isolated from mouse skeletal muscles were examined by electron microscopy. The plasma membranes of heavy ion beam-irradiated areas of muscle fibers showed irregular protrusions and invaginations. In the cytoplasm, an irregular distribution of microfilaments was found near the plasma membrane. Sarcoplasmic reticula in the irradiated regions showed a distended appearance with flocculent material within the lumen. These changes were seen as early as 2 min after irradiation, and persisted until as late as 22 min after irradiation. Many autophagic vacuoles could be seen at 7 min after irradiation. At 22 min, the vacuoles became more prominent and showed more variety. These observations suggest that heavy ion beam irradiation causes disruption of the cellular architecture and the autophagy is involved in removal of this disruption.