Muscle samples from 24 horses with polysaccharide storage myopathy were stained with periodic acid-Schiff (PAS) stain and were immunostained for ubiquitin. Abnormalities detected with PAS stain were coarse granular cytoplasmic aggregates of amylase sensitive glycogen, subsarcolemmal aggregates of glycogen, central amylase sensitive bodies, and a variety of subsarcolemmal to intracytoplasmic amylase resistant polyglucosan inclusions. All amylase resistant inclusions were positive for ubiquitin. Ubiquitin was also detected in many amylase sensitive inclusions. Based on morphologic findings and pattern of ubiquitin staining, a sequence of events, beginning with abnormal glycogen storage followed by ubiquitination and eventual development of amylase resistance, is proposed.