The aim of the present study was to determine the effect of the genetic group of the Holstein–Friesian (HF) and pasture-based feeding system (3 × 2 factorial arrangement) on locomotion score (six gait aspects scored from one to five), clinical lameness and hoof disorders within a seasonal calving milk production system. The three genetic groups compared had an average Economic Breeding Index (EBI) value of 40, 70 and 80: representing the Irish national average genetic merit (LOW-NA), high EBI genetic merit of North American ancestry (HIGH-NA) and high EBI genetic merit of New Zealand ancestry (HIGH-NZ), respectively. Two feed systems were compared: a high grass allowance, low-concentrate system typical of spring-calving herds in Ireland (control) and a high-concentrate system. Data from 126 cows collected across a complete lactation period were analysed using generalised estimating equations and survival analysis. Genetic group of HF had a significant effect on locomotion score, clinical lameness and hoof disorders. Higher EBI cows (HIGH-NA and HIGH-NZ) had lower hazard of poor locomotion score in some gait aspects (e.g. spine curvature) and lower odds of clinical lameness in the first 200 days post-calving (Odds ratios 0.08 and 0.24, respectively, relative to the LOW-NA) and some hoof disorders (e.g. traumatic lesions) compared with LOW-NA cows. The high-concentrate feed system showed a higher incidence and severity of digital dermatitis (P < 0.01). Thus, high EBI cows have better locomotion, fewer cases of clinical lameness and less-severe hoof disorders (i.e. digital dermatitis, white line disease and traumatic lesions) than low EBI cows. These findings have important implications for cow welfare and productivity.