Pathological and biochemical observations are presented in a 55-year-old woman with lupus erythematosus and thymoma who developed a vacuolar myopathy while being treated with chloroquine. Electromyography showed prominent spontaneous muscle activity including myotonic discharges. Vacuoles were present in all fibre types but, in contrast to previous cases of chloroquine myopathy, were most prominent in intermediate fibres. Electron microscopy showed cytoplasmic sequestration by membranes in proximity to the t-system, many autophagic vacuoles, tubular networks, and a variety of membranous bodies, some identical to those found in certain forms of cerebral lipidosis. Other features not previously described in chloroquine myopathy included prominent mitochondrial vacuolation and sequestration of glycogen within mitochondria. Thin-layer chromatography of muscle homogenates showed an increase in all major neutral and phospholipid fractions.