A recent study on Noriker horses reported a carrier frequency of 0.34 for the mutant H-allele of the glycogen synthase 1 (GYS-1) gene in a sample of mares and breeding stallions. The present study aimed to identify possible effects of the H-allele on exercise tolerance and performance parameters. In the annual stallion selection at the station in Stadl Paura (Upper Austria), the performance potential of twelve three-year-old Austrian Norikers (nine wildtype R/R, three heterozygous R/H) was assessed in driving, drafting and riding. The magnitude of exercise-induced stress was evaluated by the level of salivary cortisol. The exercise intensity was estimated based on maximal heart rate (HRmax) during riding and drafting. HRmax in the heterozygous horses (R/H) was 171 10 beats/min after riding and 169 20 beats/min after drafting. Salivary cortisol concentrations of these horses were 1.23 +/- 0.62 ng/ml after drafting and 3.21 +/- 0.82 ng/ml after riding. During riding, the wildtype horses (R/R) had HRmax of 163 19 beats/min and salivary cortisol concentrations of 2.40 +/- 1.40 ng/ml, while during drafting the HRmax was 160 32 beats/min and the salivary cortisol 1.02 +/- 0.35 ng/ml. We also examined the performance traits of 188 Noriker stallions. R/R (p=0.007) and R/H (p=0.006) horses had a significantly better exercise capacity than H/H Norikers. Noriker horses with two H-alleles had slightly but significantly worse gaits than R/R (p=0.043) and R/H (p=0.009) colts. In conclusion, there are some indications that Norikers with an H-allele are less resilient and have a worse exercise capacity.