The aim of this study was to determine the prevalence of equine polysaccharide storage myopathy (EPSM) in two populations of horses in the UK. Biopsy specimens from 94 horses presented to an abattoir (population 1), and 46 horses with neuromuscular disorders presented to a university referral hospital (population 2) were obtained over a period of 4years. Histological sections were examined by a veterinary pathologist for lesions including abnormal polysaccharide inclusions in myofibres. In population 1, a diagnosis of EPSM was made in 8% and non-specific myopathy in 33% of horses. In population 2, a diagnosis of EPSM was made in 22%, equine motor neurone disease (EMND) in 15% and non-specific myopathy in 37%. Within each population there was no difference in age, sex or breed distribution and muscle disease diagnosis. However, populations differed from each other in age and breed distributions and muscle disease diagnosis. EPSM was found in draft, Warmblood and related breeds and was diagnosed for the first time in cob-types. EMND was reported in 7/46 horses presented for neuromuscular disease and weakness, representing an important diagnosis in the UK. This study showed a high prevalence of EPSM and other myopathies in typical breeds of horses in the UK.