Gait analysis by accelerometry (trot, canter, and walk) of 1477 young jumping horses was recorded during 27 events in 2015 and 2016. Genetic analysis used mixed model methodology with an animal model involving 10,907 ancestors for the animal effect and velocity, sex, age, event for the fixed effects. Genetic correlations with jumping were calculated using all performances in competition since birth year 1998, i.e. 23,2952 horses, 406,750 ancestors and 458,269 annual performances from 2002 to 2016. Genome-wide analysis was performed including 541,175 SNP after quality control. Results showed a high heritability for dorsoventral displacement and stride frequency (>0.41), moderate for longitudinal activity (>0.19) and low for lateral activity (<0.07). The same characteristics at trot and canter were genetically correlated (>0.56). Genetic correlation with jumping performance was null except one negative correlation (-0.22*) for longitudinal activity at canter. GWAS revealed the importance of withers height on gaits and explained the choice to include this trait as covariate to investigate gaits at constant height and velocity. For the breeding objective, the selection of jumping horse is nearly independent of the gait characteristics except longitudinal activity at the canter.