Chloroquine, an anti-malaria drug, is known to cause myopathy with rimmed vacuole formation. Although it disrupts the lysosomal degradation of proteins, the precise mechanism underlying muscle fiber degeneration has remained unclear. We investigated the temporal profiles of muscle fiber degeneration in chloroquine-treated rats, paying special attention to endoplasmic reticulum (ER) stress and autophagy. Male Wistar rats were intraperitoneally injected with chloroquine diphosphate at a dosage of 50 mg/kg body weight every day. We examined the localization and levels of proteins related to ER stress and autophagy in soleus muscle by means of immunohistochemistry and Western blotting at 3, 5, and 7 weeks after the beginning of the treatment. At 3 weeks, the levels of LC3-II and amyloid-beta (Abeta) were increased. At 5 weeks, an unfolded protein response took place. At 7 weeks, rimmed vacuole formation became obvious. Interestingly, SERCA2, a Ca2+ -pump ATPase located in the endoplasmic/sarcoplasmic reticulum membrane was up-regulated at 5 weeks after treatment, but declined to the control level by 7 weeks. Taken together, these findings suggest that Abeta accumulation (at 3 weeks) caused by the disruption of lysosomal enzymes precedes an unfolded protein response (at 5 weeks). Next, activation of autophagy occurs (at 7 weeks), probably using sarcoplasmic reticulum membrane, the amount of which was increased. Chloroquine-treated rats could be useful for investigating the pathogenesis of diseases related to Abeta accumulation.