The prevalence of vertical asymmetries is high in “owner-sound” warmblood riding horses, however the origin of these asymmetries is unknown. This study investigated correlations between vertical asymmetries and motor laterality. Young warmblood riding horses (N = 65), perceived as free from lameness were evaluated on three visits, each comprising objective gait analysis (inertial measurement units system) and a rider questionnaire on perceived sidedness of the horse. A subgroup (N = 40) of horses were also subjected to a forelimb protraction preference test intended as an assessment of motor laterality. We hypothesized associations between vertical asymmetry and motor laterality as well as rider-perceived sidedness. Vertical asymmetry was quantified as trial means of the stride-by-stride difference between the vertical displacement minima and maxima of the head (HDmin, HDmax) and pelvis (PDmin, PDmax). Laterality indexes, based on counts of which limb was protracted, and binomial tests were used to draw conclusions from the preference tests. In the three visits, 60–70% of horses exhibited vertical asymmetries exceeding clinically used thresholds for ≥1 parameter, and 22% of horses exhibited a side preference in the preference test as judged by binomial tests. Linear mixed models identified a weak but statistically significant correlation between perceived hindlimb weakness and higher PDmin values attributable to either of the hindlimbs (p = 0.023). No other statistically significant correlations to vertical asymmetry were seen for any of the questionnaire answers tested. Tests of correlation between the absolute values of laterality index and asymmetry parameters (HDmin, HDmax, PDmin, PDmax) identified a weak correlation (p = 0.049) with PDmax, but when accounting for the direction of asymmetry and motor laterality, no correlations were seen for either of the asymmetry parameters. No convincing evidence of associations between vertical asymmetries and motor laterality were seen and further studies investigating motor laterality and the origin of vertical asymmetries are needed.