The aim of this study was to determine the occurrence and frequency of a mutation in the gene coding for skeletal muscle glycogen synthase type 1 (GYS-1), which is the cause of equine polysaccharide storage myopathy (PSSM) type 1 in a population of 50 Haflingers. GYS-1 genotyping of 50 Haflingers was performed with a validated restriction fragment length polymorphism (RFLP) assay. The second aim was to compare resting and post-exercise muscle enzyme activities as well as parameters of glucose metabolism in blood between horses with and without the mutation. Nine of the 50 Haflingers were identified to be heterozygous for the mutation (HR). None was homozygous (HH). The estimated HR prevalence was 18 per cent in this herd. Mean aspartate aminotransferase (AST) activity at rest and mean creatine kinase and AST activity after exercise were significantly higher in HR compared with RR (homozygote normal) horses. No significant differences could be found in the other parameters.