The existence of sexual dimorphism in the Minorcan horse, an autochthonous breed from Minorca Island in the Balearic archipelago (NW Mediterranean Sea), is established in the official standard, with females being shorter and longer than males as well as having slenderer necks and a squarer croup. However, no study so far has explored the size and shape components of this dimorphism separately. The aim of this study was to analyse the morphology of this breed using geometric morphometric methods in order to find size and shape differences between sire lines. The analysis was based on landmarks digitized in lateral view from 38 registered adult Minorcan horses (20 males and 18 females) within an age range of 3–14 years (average 7 years) with different performance goals. The analyses did not reveal any significant differences between the “shape” and “size” of male and female animals, for the landmarks studied, so the sexes are functionally similar.