We examined the relationship between inherited motor-related conformation and orientation of facial hair whorls in Japanese Kiso horses. Eleven horses were divided into clockwise, counterclockwise, and radial groups according to facial hair whorls. We placed six markers on anatomical landmarks of each lateral side in a horse and measured the height of the landmarks, the distance between adjacent landmarks, and the angle of the adjacent landmarks. In the counterclockwise group, the horses tended to exhibit higher values on the left side than on the right side, and the comparison of the height of landmarks revealed a significant difference between both sides. Therefore, the orientation of facial hair whorls may suggest the tendency of motor-related conformation, at least in counterclockwise group.