Objective of the study was to assess histopathological changes in horses with a clinical history of exertional rhabdomyolysis (ER) with special reference to polysaccharide storage myopathy and to compare histopathological findings in horses with and without a clinical history of ER. In total 39 muscle samples were collected, from horses with a history of repeated episodes of exertional rhabdomyolysis (test group, 10 horses) and from horses without clinical signs of muscular disorders in their history (control group, 29 horses). Frozen muscle samples were stained with haematoxylin and eosin and periodic acid-Schiff with and without amylase digestion. Histopathologic changes (amylase resistant polysaccharide, subsarcolemmal glycogen, intracytoplasmic masses, subsarcolemmal vacuoles, fibre size variation and internal nuclei) were evaluated. There was a statistically significant difference between groups in the presence of subsarcolemmal amylase sensitive glycogen deposits (P ≤ 0.0001), the risk ratio was 5.22. Statistically significant differences between groups were not found regarding the presence of intracytoplasmic masses, subsarcolemmal vacuoles, amylase resistant polysaccharide, fibre size variation and internal nuclei. Presence of amylase resistant polysaccharide within muscle fibres of apparently healthy horses could be a manifestation of different phenotype expression of PSSM but also the insufficient specificity of this diagnostic criterion.